I definitely think that - as mentioned on the episode thread - the Judoon could come back.
I can imagine them popping up from time to time, gradually getting to know and trust The Doctor, and then calling on him for help - or maybe vice versa, as The Doctor is a bit dismissive of them right now but they could prove useful allies at some point.
If The Master was ever to return, and is Moriarty to The Doctor's Holmes, perhaps the Judoon could be Inspector Lestrade?