I dont think Doctor Who can really crossover with anything, but they could do a Whoverse Law&Order like they have done Eastenders.
Actually I think Doctor Who is probably the easiest show to crossover to another franchise. He would fit in anywhere.
Typically an episode of Doctor Who starts with the guest cast, and then about 5-10 minutes into the episode the Doctor and companion(s) show up for no reason. That format would work for anything.
The Scooby Gang are in the library? The Doctor shows up.
Xena's battling Ares? The Doctor shows up.
George and Jerry are eating in the diner? The Doctor shows up.
Batman's fighting the Joker? The Doctor shows up.
Teal'c returns to Chulak? The Doctor shows up.