When I leave I'm not going to pay my roommates' application fees to reapply for our apartment.
Is there a reason you came to this conclusion?
He turned out to be a massive hypocrite and showed no interest in helping my relationship with the landlord.
That is fine since you are no longer going to be living with him. There is no need to pay the fees of someone that you will not be living with anymore.
Thanks, though I know it will annoy the shit out of him by leaving him with the fees.
While your motives might not be completely pure if you are no longer going to be living in the apartment then it's his responsibility to pay the fees for his living arrangement. It would be kind to give him a heads up so he isn't taken off guard, but otherwise once you move out then you have no obligation to pay.