For along time I'd wanted to see a Star Trek/Star Wars crossover, but I've lost interest in that as time has gone on. Instead I would love to see a Stargate/Star Trek crossover, I think the two could actually work really well together. And for some reason I was thinking that Star Trek/Farscape could be cool. I honestly don't know where that came form, it just sorta popped into my head. Star Trek/Dr. Who would also work.
Star Trek/DW has more or less been done numerous times on both sides - you could easily make the spaceship crew in Planet Of Evil a Starfleet crew, or replace Guinan in Time's Arrow with the Doctor, with only minor rewriting.
Stargate would work better as a DW or Torchwood crossover than with Trek (come on, a cliffhanger with Daleks flooding through the Gate would be fab!)
Highlander would work, but I'd really like to see a Buffy (or Angel)/Highlander crossover more than a Trek one...