In the 90s I liked to think Seaquest DSV took place in the Star Trek universe. I would read that comic crossover.
There are a lot of similarities aren't there?
Stargate SG1/Star Trek TOS could be excellent, just to see how the characters would interact.
People have always said I'd enjoy SG1 but I've never seen it. I'd welcome a crossover as a "way in"
Back when Babylon 5 was running, I thought that a crossover with TOS could be fun. I doubt there'd be much of a market for it now.
Wouldn't a B5/TNGorDS9 crossover suit more?
Or maybe IDW could team up with Dynamite and do a Battlestar Galactica crossover, or a Firefly/Serenity one with Dark Horse...
Just read a Galaxy Quest comic last week. They'd go well together.
Star Trek/Star Wars
I'm still holding out hope for a Star Trek / Star Wars crossover, but it's not very likely since Star Wars is a lot less crossover-friendly than Star Trek. Soulcalibur IV is the only intercompany crossover than Star Wars has participated in.
Regarding Star Trek/Star Wars:
I always thought they should do a 2 issue mini. The first issue would end with some space/time thing weakening the boundaries between universes which could lead to several one-shots of different ST/SW eras crossing over.
A lot of these are very doable. Just browse the web, you'll find hundreds of fan fictions. Star Wars/Star Trek seems the most obvious but the last time Marvel did an intercompany crossover was 2004, so over a decade ago.
A lot of these ideas I'd be very interested in!
My favourite crossover so far has been Star Trek/Green Lantern as it really mashes both mythologies well. I admit Assimilation2 was the only other story where I knew the other property really well but I felt the story dragged in the middle issues.