If they were still on the air, I'd like to see a Doctor Who crossover with either "Star Trek: Voyager" or "Babylon 5".
However, since they're not, I'll go with a Doctor Who crossover with "The Walking Dead". I think it'd be interesting. If the Doctor got bit, would be become a zombie? Would he regenerate? Would whatever companion currently traveling with him still have the hots for him if the flesh was falling off his face?
Doctor: Oh, no, I've become a zombie. Am I still young and sexy?
Companion: Sorry, no. Bye!
Also, a special bonus would be an appearance by The Governor, also known as Jackson Lake.