You can use DBCA or manual scripts to create a container database (CDB).
However in both cases these tools will create a database with all database options like JServer, APEX, etc. I don't think that it is possible to use DBCA in graphical mode to create a database without any option. I don't know if you can use CREATE DATABASE SQL statement with catcdb.sql to create such a database.

Mike Dietrich has published on his upgrade blog a way to create a CDB without any database option using DBCA with a mix of graphical steps and manual editing of generated files: this way of doing is supported by Oracle Corp.

In this blog post I show that it is possible to use DBCA in command line mode to create a CDB without any database option.

For this article I have used Oracle Database Entreprise Edition 12.1.0.2 (without any PSU) on Oracle Linux 6.4 (VirtualBox 5.0.4).

I have coded a script named dbca.sh which does the following:

runs DBCA in silent mode to generate the different database creation scripts in $ORACLE_BASE/admin/<DB>/scripts
removes all database options statements from <DB>.sql
modifies <DB>.sql to avoid SYS password prompt for orapwd command
modifies CreateDBCatalog.sql to remove Workspace Manager option
adds sysPassword and systemPassword SQL*Plus variables to $SQLPATH/login.sql to avoid modifying other SQL scripts

modifies postDBCreation.sql to fix a bug for ASM SPFILE file name which is not correctly set:

SYS@CNODB>create spfile='+DATA' FROM pfile='/u01/app/oracle/admin/CNODB/scripts/init.ora';

File created.

At next instance startup fails:

SYS@CNODB>startup ;
ORA-01078: failure in processing system parameters
ORA-01565: error in identifying file '+DATA/CNODB/spfileCNODB.ora'
ORA-17503: ksfdopn:2 Failed to open file +DATA/CNODB/spfileCNODB.ora
ORA-15056: additional error message
ORA-17503: ksfdopn:2 Failed to open file +DATA/CNODB/spfilecnodb.ora
ORA-15173: entry 'spfilecnodb.ora' does not exist in directory 'CNODB'
ORA-06512: at line 4

My script dbca.sh has following prerequisites:

ORACLE_HOME, ORACLE_BASE and SQLPATH must be defined
$SQLPATH/login.sql must be writable

Following items are hard-coded:

Database is using ASM storage
No pluggable database is created
RAC database is not taken into account

The script source code is here.

Here is the script output (it has taken about 35 minutes to created the database in my environment):

$ ./dbca.sh -dbname CDB -cset AL32UTF8 -password oracle -dgname DATA -rgname FRA -mempc 20
Database creation script generation
1% complete
3% complete
7% complete
8% complete
10% complete
12% complete
13% complete
14% complete
15% complete
17% complete
23% complete
28% complete
33% complete
35% complete
36% complete
37% complete
39% complete
40% complete
50% complete
53% complete
54% complete
60% complete
67% complete
71% complete
75% complete
82% complete
89% complete
90% complete
93% complete
96% complete
100% complete
Look at the log file "/u01/app/oracle/admin/CDB/scripts/CDB.log" for further details.
You should Add this entry in the /etc/oratab: CDB:/u01/app/12.1.0.2/db:Y

SQL*Plus: Release 12.1.0.2.0 Production on Wed Nov 11 12:00:23 2015

Copyright (c) 1982, 2014, Oracle.  All rights reserved.



Connected to an idle instance.
SYS@CDB>spool /u01/app/oracle/admin/CDB/scripts/CreateDB.log append
SYS@CDB>startup nomount pfile="/u01/app/oracle/admin/CDB/scripts/init.ora";
ORACLE instance started.

Total System Global Area  830472192 bytes
Fixed Size                  2929840 bytes
Variable Size             624954192 bytes
Database Buffers          197132288 bytes
Redo Buffers                5455872 bytes
SYS@CDB>CREATE DATABASE "CDB"
  2  MAXINSTANCES 8
  3  MAXLOGHISTORY 1
  4  MAXLOGFILES 16
  5  MAXLOGMEMBERS 3
  6  MAXDATAFILES 1024
  7  DATAFILE SIZE 700M AUTOEXTEND ON NEXT  10240K MAXSIZE UNLIMITED
  8  EXTENT MANAGEMENT LOCAL
  9  SYSAUX DATAFILE SIZE 550M AUTOEXTEND ON NEXT  10240K MAXSIZE UNLIMITED
 10  SMALLFILE DEFAULT TEMPORARY TABLESPACE TEMP TEMPFILE SIZE 20M AUTOEXTEND ON NEXT  640K MAXSIZE UNLIMITED
 11  SMALLFILE UNDO TABLESPACE "UNDOTBS1" DATAFILE  SIZE 200M AUTOEXTEND ON NEXT  5120K MAXSIZE UNLIMITED
 12  CHARACTER SET AL32UTF8
 13  NATIONAL CHARACTER SET AL16UTF16
 14  LOGFILE GROUP 1  SIZE 50M,
 15  GROUP 2  SIZE 50M,
 16  GROUP 3  SIZE 50M
 17  USER SYS IDENTIFIED BY "&&sysPassword" USER SYSTEM IDENTIFIED BY "&&systemPassword"
 18  enable pluggable database;

Database created.

SYS@CDB>set linesize 2048;
SYS@CDB>column ctl_files NEW_VALUE ctl_files;
SYS@CDB>select concat('control_files=''', concat(replace(value, ', ', ''','''), '''')) ctl_files from v$parameter where name ='control_files';

CTL_FILES
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
control_files='+DATA/CDB/CONTROLFILE/current.288.895492833','+FRA/CDB/CONTROLFILE/current.258.895492833'

SYS@CDB>host echo &ctl_files >>/u01/app/oracle/admin/CDB/scripts/init.ora;

SYS@CDB>spool off
SYS@CDB>@/u01/app/oracle/admin/CDB/scripts/CreateDBFiles.sql
SYS@CDB>SET VERIFY OFF
SYS@CDB>connect "SYS"/"&&sysPassword" as SYSDBA
Connected.
SYS@CDB>set echo on
SYS@CDB>spool /u01/app/oracle/admin/CDB/scripts/CreateDBFiles.log append
SYS@CDB>CREATE SMALLFILE TABLESPACE "USERS" LOGGING  DATAFILE  SIZE 5M AUTOEXTEND ON NEXT  1280K MAXSIZE UNLIMITED  EXTENT MANAGEMENT LOCAL  SEGMENT SPACE MANAGEMENT  AUTO;

Tablespace created.

SYS@CDB>ALTER DATABASE DEFAULT TABLESPACE "USERS";

Database altered.

SYS@CDB>spool off
SYS@CDB>@/u01/app/oracle/admin/CDB/scripts/CreateDBCatalog.sql
SYS@CDB>SET VERIFY OFF
SYS@CDB>connect "SYS"/"&&sysPassword" as SYSDBA
Connected.
SYS@CDB>set echo on
SYS@CDB>spool /u01/app/oracle/admin/CDB/scripts/CreateDBCatalog.log append
SYS@CDB>alter session set "_oracle_script"=true;

Session altered.

SYS@CDB>alter pluggable database pdb$seed close;

Pluggable database altered.

SYS@CDB>alter pluggable database pdb$seed open;

Pluggable database altered.

SYS@CDB>host perl /u01/app/12.1.0.2/db/rdbms/admin/catcon.pl -n 1 -l /u01/app/oracle/admin/CDB/scripts -b catalog /u01/app/12.1.0.2/db/rdbms/admin/catalog.sql;
catcon: ALL catcon-related output will be written to /u01/app/oracle/admin/CDB/scripts/catalog_catcon_13257.lst
catcon: See /u01/app/oracle/admin/CDB/scripts/catalog*.log files for output generated by scripts
catcon: See /u01/app/oracle/admin/CDB/scripts/catalog_*.lst files for spool files, if any
catcon.pl: completed successfully

SYS@CDB>host perl /u01/app/12.1.0.2/db/rdbms/admin/catcon.pl -n 1 -l /u01/app/oracle/admin/CDB/scripts -b catproc /u01/app/12.1.0.2/db/rdbms/admin/catproc.sql;
catcon: ALL catcon-related output will be written to /u01/app/oracle/admin/CDB/scripts/catproc_catcon_13342.lst
catcon: See /u01/app/oracle/admin/CDB/scripts/catproc*.log files for output generated by scripts
catcon: See /u01/app/oracle/admin/CDB/scripts/catproc_*.lst files for spool files, if any
catcon.pl: completed successfully

SYS@CDB>host perl /u01/app/12.1.0.2/db/rdbms/admin/catcon.pl -n 1 -l /u01/app/oracle/admin/CDB/scripts -b catoctk /u01/app/12.1.0.2/db/rdbms/admin/catoctk.sql;
catcon: ALL catcon-related output will be written to /u01/app/oracle/admin/CDB/scripts/catoctk_catcon_14163.lst
catcon: See /u01/app/oracle/admin/CDB/scripts/catoctk*.log files for output generated by scripts
catcon: See /u01/app/oracle/admin/CDB/scripts/catoctk_*.lst files for spool files, if any
catcon.pl: completed successfully

SYS@CDB>
SYS@CDB>host perl /u01/app/12.1.0.2/db/rdbms/admin/catcon.pl -n 1 -l /u01/app/oracle/admin/CDB/scripts -b pupbld -u SYSTEM/&&systemPassword /u01/app/12.1.0.2/db/sqlplus/admin/pupbld.sql;
catcon: ALL catcon-related output will be written to /u01/app/oracle/admin/CDB/scripts/pupbld_catcon_14227.lst
catcon: See /u01/app/oracle/admin/CDB/scripts/pupbld*.log files for output generated by scripts
catcon: See /u01/app/oracle/admin/CDB/scripts/pupbld_*.lst files for spool files, if any
catcon.pl: completed successfully

SYS@CDB>connect "SYSTEM"/"&&systemPassword"
Connected.
SYSTEM@CDB>set echo on
SYSTEM@CDB>spool /u01/app/oracle/admin/CDB/scripts/sqlPlusHelp.log append
SYSTEM@CDB>host perl /u01/app/12.1.0.2/db/rdbms/admin/catcon.pl -n 1 -l /u01/app/oracle/admin/CDB/scripts -b hlpbld -u SYSTEM/&&systemPassword -a 1  /u01/app/12.1.0.2/db/sqlplus/admin/help/hlpbld.sql 1helpus.sql;
catcon: ALL catcon-related output will be written to /u01/app/oracle/admin/CDB/scripts/hlpbld_catcon_14320.lst
catcon: See /u01/app/oracle/admin/CDB/scripts/hlpbld*.log files for output generated by scripts
catcon: See /u01/app/oracle/admin/CDB/scripts/hlpbld_*.lst files for spool files, if any
catcon.pl: completed successfully

SYSTEM@CDB>spool off
SYSTEM@CDB>spool off
not spooling currently
SYSTEM@CDB>--
SYSTEM@CDB>--
SYSTEM@CDB>--
SYSTEM@CDB>--
SYSTEM@CDB>--
SYSTEM@CDB>--
SYSTEM@CDB>--
SYSTEM@CDB>--
SYSTEM@CDB>--
SYSTEM@CDB>@/u01/app/oracle/admin/CDB/scripts/CreateClustDBViews.sql
SYSTEM@CDB>SET VERIFY OFF
SYSTEM@CDB>connect "SYS"/"&&sysPassword" as SYSDBA
Connected.
SYS@CDB>set echo on
SYS@CDB>spool /u01/app/oracle/admin/CDB/scripts/CreateClustDBViews.log append
SYS@CDB>host perl /u01/app/12.1.0.2/db/rdbms/admin/catcon.pl -n 1 -l /u01/app/oracle/admin/CDB/scripts -b catclust /u01/app/12.1.0.2/db/rdbms/admin/catclust.sql;
catcon: ALL catcon-related output will be written to /u01/app/oracle/admin/CDB/scripts/catclust_catcon_14387.lst
catcon: See /u01/app/oracle/admin/CDB/scripts/catclust*.log files for output generated by scripts
catcon: See /u01/app/oracle/admin/CDB/scripts/catclust_*.lst files for spool files, if any
catcon.pl: completed successfully

SYS@CDB>spool off
SYS@CDB>connect "SYS"/"&&sysPassword" as SYSDBA
Connected.
SYS@CDB>set echo on
SYS@CDB>spool /u01/app/oracle/admin/CDB/scripts/postDBCreation.log append
SYS@CDB>grant sysdg to sysdg;

Grant succeeded.

SYS@CDB>grant sysbackup to sysbackup;

Grant succeeded.

SYS@CDB>grant syskm to syskm;

Grant succeeded.

SYS@CDB>host echo "SPFILE='+DATA/CDB/spfileCDB.ora'" > /u01/app/12.1.0.2/db/dbs/initCDB.ora

SYS@CDB>@/u01/app/oracle/admin/CDB/scripts/lockAccount.sql
SYS@CDB>SET VERIFY OFF
SYS@CDB>connect "SYS"/"&&sysPassword" as SYSDBA
Connected.
SYS@CDB>set echo on
SYS@CDB>spool /u01/app/oracle/admin/CDB/scripts/lockAccount.log append
SYS@CDB>alter session set "_oracle_script"=true;

Session altered.

SYS@CDB>alter pluggable database pdb$seed close;

Pluggable database altered.

SYS@CDB>alter pluggable database pdb$seed open;

Pluggable database altered.

SYS@CDB>BEGIN
  2   FOR item IN ( SELECT USERNAME FROM DBA_USERS WHERE ACCOUNT_STATUS IN ('OPEN', 'LOCKED', 'EXPIRED') AND USERNAME NOT IN (
  3  'SYS','SYSTEM') )
  4   LOOP
  5    dbms_output.put_line('Locking and Expiring: ' || item.USERNAME);
  6    execute immediate 'alter user ' ||
  7           sys.dbms_assert.enquote_name(
  8           sys.dbms_assert.schema_name(
  9           item.USERNAME),false) || ' password expire account lock' ;
 10   END LOOP;
 11  END;
 12  /

PL/SQL procedure successfully completed.

SYS@CDB>alter session set container=pdb$seed;

Session altered.

SYS@CDB>BEGIN
  2   FOR item IN ( SELECT USERNAME FROM DBA_USERS WHERE ACCOUNT_STATUS IN ('OPEN', 'LOCKED', 'EXPIRED') AND USERNAME NOT IN (
  3  'SYS','SYSTEM') )
  4   LOOP
  5    dbms_output.put_line('Locking and Expiring: ' || item.USERNAME);
  6    execute immediate 'alter user ' ||
  7           sys.dbms_assert.enquote_name(
  8           sys.dbms_assert.schema_name(
  9           item.USERNAME),false) || ' password expire account lock' ;
 10   END LOOP;
 11  END;
 12  /

PL/SQL procedure successfully completed.

SYS@CDB>alter session set container=cdb$root;

Session altered.

SYS@CDB>spool off
SYS@CDB>@/u01/app/oracle/admin/CDB/scripts/postDBCreation.sql
SYS@CDB>SET VERIFY OFF
SYS@CDB>spool /u01/app/oracle/admin/CDB/scripts/postDBCreation.log append
SYS@CDB>host perl /u01/app/12.1.0.2/db/rdbms/admin/catcon.pl -n 1 -l /u01/app/oracle/admin/CDB/scripts -b catbundleapply /u01/app/12.1.0.2/db/rdbms/admin/catbundleapply.sql;
catcon: ALL catcon-related output will be written to /u01/app/oracle/admin/CDB/scripts/catbundleapply_catcon_14464.lst
catcon: See /u01/app/oracle/admin/CDB/scripts/catbundleapply*.log files for output generated by scripts
catcon: See /u01/app/oracle/admin/CDB/scripts/catbundleapply_*.lst files for spool files, if any
catcon.pl: completed successfully

SYS@CDB>connect "SYS"/"&&sysPassword" as SYSDBA
Connected.
SYS@CDB>set echo on
SYS@CDB>create spfile='+DATA/CDB/spfileCDB.ora' FROM pfile='/u01/app/oracle/admin/CDB/scripts/init.ora';

File created.

SYS@CDB>connect "SYS"/"&&sysPassword" as SYSDBA
Connected.
SYS@CDB>host perl /u01/app/12.1.0.2/db/rdbms/admin/catcon.pl -n 1 -l /u01/app/oracle/admin/CDB/scripts -b utlrp /u01/app/12.1.0.2/db/rdbms/admin/utlrp.sql;
catcon: ALL catcon-related output will be written to /u01/app/oracle/admin/CDB/scripts/utlrp_catcon_14535.lst
catcon: See /u01/app/oracle/admin/CDB/scripts/utlrp*.log files for output generated by scripts
catcon: See /u01/app/oracle/admin/CDB/scripts/utlrp_*.lst files for spool files, if any
catcon.pl: completed successfully

SYS@CDB>select comp_id, status from dba_registry;

COMP_ID                        STATUS
------------------------------ --------------------------------------------
XDB                            VALID
CATALOG                        VALID
CATPROC                        VALID
RAC                            OPTION OFF

SYS@CDB>shutdown immediate;
Database closed.
Database dismounted.
ORACLE instance shut down.
SYS@CDB>connect "SYS"/"&&sysPassword" as SYSDBA
Connected to an idle instance.
SYS@CDB>startup ;
ORACLE instance started.

Total System Global Area  830472192 bytes
Fixed Size                  2929840 bytes
Variable Size             633342800 bytes
Database Buffers          188743680 bytes
Redo Buffers                5455872 bytes
Database mounted.
Database opened.
SYS@CDB>spool off
SYS@CDB>exit;
Disconnected from Oracle Database 12c Enterprise Edition Release 12.1.0.2.0 - 64bit Production
With the Partitioning, Automatic Storage Management, OLAP, Advanced Analytics
and Real Application Testing options

CDB successfully created..

Because /etc/oratab is writable, dbca.sh has updated it:

$ tail -2 /etc/oratab
+ASM:/u01/app/12.1.0.2/grid:N           # line added by Agent
CDB:/u01/app/12.1.0.2/db:N # added by dbca.sh
$

login.sql has been restored by dbca.sh:

$ cat login.sql
set sqlprompt "&&_USER@&&_CONNECT_IDENTIFIER>"

I have checked the created database with following SQL statements:

SYS@CDB>select name, cdb from v$database;

NAME      CDB
--------- ---
CDB       YES

SYS@CDB>select comp_id, comp_name, version, status from dba_registry;

COMP_ID         COMP_NAME                                VERSION    STATUS
--------------- ---------------------------------------- ---------- ----------
XDB             Oracle XML Database                      12.1.0.2.0 VALID
CATALOG         Oracle Database Catalog Views            12.1.0.2.0 VALID
CATPROC         Oracle Database Packages and Types       12.1.0.2.0 VALID
RAC             Oracle Real Application Clusters         12.1.0.2.0 OPTION OFF

SYS@CDB>show pdbs

    CON_ID CON_NAME                       OPEN MODE  RESTRICTED
---------- ------------------------------ ---------- ----------
         2 PDB$SEED                       READ ONLY  NO
SYS@CDB>select * from v$pwfile_users;

USERNAME                       SYSDB SYSOP SYSAS SYSBA SYSDG SYSKM     CON_ID
------------------------------ ----- ----- ----- ----- ----- ----- ----------
SYS                            TRUE  TRUE  FALSE FALSE FALSE FALSE          0
SYSDG                          FALSE FALSE FALSE FALSE TRUE  FALSE          1
SYSBACKUP                      FALSE FALSE FALSE TRUE  FALSE FALSE          1
SYSKM                          FALSE FALSE FALSE FALSE FALSE TRUE           1

SYS@CDB>

Note that XDB is a mandatory component in Oracle Database 12c.

Database password file has been created in $ORACLE_HOME/dbs:

$ ls -al $ORACLE_HOME/dbs/orapwCDB
-rw-r----- 1 oracle oinstall 7680 Nov 11 12:34 /u01/app/12.1.0.2/db/dbs/orapwCDB

Oracle Restart local registry has also been updated by dbca.sh:

$ srvctl config database -d CDB
Database unique name: CDB
Database name:
Oracle home: /u01/app/12.1.0.2/db
Oracle user: oracle
Spfile: +DATA/CDB/spfileCDB.ora
Password file:
Domain:
Start options: open
Stop options: immediate
Database role: PRIMARY
Management policy: AUTOMATIC
Disk Groups: DATA,FRA
Services:
OSDBA group:
OSOPER group:
Database instance: CDB

I have created a pluggable database (PDB)with:

SYS@CDB>create pluggable database PDB
  2  admin user pdba identified by oracle
  3  default tablespace ts_pdb;

Pluggable database created.

SYS@CDB>alter pluggable database pdb open;

Pluggable database altered.

SYS@CDB>show pdbs

    CON_ID CON_NAME                       OPEN MODE  RESTRICTED
---------- ------------------------------ ---------- ----------
         2 PDB$SEED                       READ ONLY  NO
         3 PDB                            READ WRITE NO
SYS@CDB>

I have also checked that corresponding database service has been registered to Grid Infrastructure listener:

$ . oraenv
ORACLE_SID = [CDB] ? +ASM
The Oracle base remains unchanged with value /u01/app/oracle
$ lsnrctl status

LSNRCTL for Linux: Version 12.1.0.2.0 - Production on 11-NOV-2015 12:40:25

Copyright (c) 1991, 2014, Oracle.  All rights reserved.

Connecting to (DESCRIPTION=(ADDRESS=(PROTOCOL=IPC)(KEY=EXTPROC1521)))
STATUS of the LISTENER
------------------------
Alias                     LISTENER
Version                   TNSLSNR for Linux: Version 12.1.0.2.0 - Production
Start Date                11-NOV-2015 08:53:35
Uptime                    0 days 3 hr. 46 min. 49 sec
Trace Level               off
Security                  ON: Local OS Authentication
SNMP                      OFF
Listener Parameter File   /u01/app/12.1.0.2/grid/network/admin/listener.ora
Listener Log File         /u01/app/oracle/diag/tnslsnr/ol6twsa/listener/alert/log.xml
Listening Endpoints Summary...
  (DESCRIPTION=(ADDRESS=(PROTOCOL=ipc)(KEY=EXTPROC1521)))
  (DESCRIPTION=(ADDRESS=(PROTOCOL=tcp)(HOST=ol6twsa)(PORT=1521)))
Services Summary...
Service "+ASM" has 1 instance(s).
  Instance "+ASM", status READY, has 1 handler(s) for this service...
Service "CDB" has 1 instance(s).
  Instance "CDB", status READY, has 1 handler(s) for this service...
Service "CDBXDB" has 1 instance(s).
  Instance "CDB", status READY, has 1 handler(s) for this service...
Service "pdb" has 1 instance(s).
  Instance "CDB", status READY, has 1 handler(s) for this service...
The command completed successfully

Remember that in this container database you cannot create or plug a PDB that is using a database option that is not installed in the root container.