To stop the job before it finishes: 

qdel <job id>

You get the job id from the qstat -a or qstat -a -u <username> command.The job id is also shown just after the job starts.

In those instances where this does not work, you can instead try to send a signal to them:

qsig -s 0 $jobid

Then the batch system will checkup on them and clean them away if they are not supposed to be there.