If you really want to make a decent x-over fic in earnest (and not as a silly comedic piece per se), here are some guidelines to consider, so I do not hunt you down and cut off your fingers.
1. Both fandoms should exist in the same relative time period (time travel series like Doctor Who or Quantum Leap not withstanding).
2. The Universes should be compatible. Sure, you want to do a crossover with your two favourite magic-using fandoms. But if the rules of how the magic works are too different in the two fandoms, it just creates too many problems. Same with certain Sci-Fi. And then there are certain Universes I can't see being compatible with anything else such as Star Wars, Farscape, or Lord of the Rings.
3. They should also be compatible thematically. Crossover crime-investigation shows (CSI/Bones), alien intrigues (X-Files/Roswell), or 60s Spy shows (why haven't I seen a Man from UNCLE/The Avengers x-over yet?). Or several permutations of comic-book heroes (hell, they do it enough in the canon...)
4. DO NOT CROSSOVER FANDOMS JUST BECAUSE THEY SHARE AN ACTOR!!!!! If I see one of those NCIS/Sapphire & Steel fics recced on
crack_van one more time, I will poke their goddam eyes out! *heavy angry breathing* That just totally breaks rule #3 there.
5. RPF...just no.
6. If the crossover requires you to change character histories/personalities from one fandom or the other to make it work...then just don't bother.
7. If one show references another, thereby rendering that universe fictional, do not cross them over. For example, in Life on Mars, Sam mentions Doctor Who. Therefore I cannot accept a LoM/DW crossover. Just as some of those fics that try to make it that NCIS' Ducky is a retired Illya cannot fly. When asked what Ducky looked like when he was younger, Gibbs responds "Illya Kuryakin." As in the the 60s sex symbol, and not as a person that could have existed in the NCIS 'verse. 'cause that's just be silly and render the remark meaningless.
Now I will give that there may be exceptions to these rules. Someone out there was brilliant enough to make a crossover that normaly wouldn't work believable. It's just rare.