Run a SQL statement on all databases monitored by OEM
First you need to set the preferred credentials for the targets. After that, you can use emcli for this. In the below example I have a group called sandbox_databases containing 3 databases:

$ emcli login -username=sysman
$ emcli execute_sql -sql="select count(*) from dba_users" -targets="sandbox_databases:group"


And the output is:

*******************************************************************************
* Target: XXXXX1:oracle_database
* Execution Status: Succeeded
*******************************************************************************

  COUNT(*)
----------
         9


*******************************************************************************
* Target: XXXXX2:oracle_database
* Execution Status: Succeeded
*******************************************************************************

  COUNT(*)
----------
        12


*******************************************************************************
* Target: XXXXX3:oracle_database
* Execution Status: Succeeded
*******************************************************************************

  COUNT(*)
----------
        10


*******************************************************************************
* Execution Summary
*     Targets Succeeded: 3
*         XXXXX1:oracle_database,XXXXX2:oracle_database,XXXXX3:oracle_database
*     Targets Failed: 0
*******************************************************************************


ALTER commands also work, for example:

$ emcli execute_sql -sql="alter user bp account lock" -targets="another_group:group"
*******************************************************************************
* Target: XXXXX4:rac_database
* Execution Status: Succeeded
*******************************************************************************

PL/SQL procedure successfully completed.


User altered.


*******************************************************************************
* Execution Summary
*     Targets Succeeded: 1
*         XXXXX4:rac_database
*     Targets Failed: 0
*******************************************************************************