I once started on a Doctor Who/Star Trek: Voyager fanfic, although I never finished it. I liked it for 4 main reasons:
1.) Daleks vs. Borg. vs. Cybermen, oh my!
2.) The cheap humor opportunities when the Doctor (David Tennant) meets the Doctor (Robert Picardo).
3.) I thought Seven of Nine would make a good companion.
4.) I was able to dovetail the universes very nicely, tying in the stuff with the Daleks & the Cybermen in the void in "Army of Ghosts"/"Doomsday" with the Borg's search for new lifeforms to assimilate in alternate dimensions (SEE Species 8472 in "Scorpion").
I had an idea for an Early Edition/Wonderfalls crossover where Gary Hobson goes on vacation to Niagara Falls. Due to an unforseeable chain of events, Jaye Tyler accidentally injures Gary. With Gary in the hospital, it's now up to Jaye to use Gary's paper to help people, while still dealing with the talking animals that won't leave her alone.
Back in high school, I came up with an epic 7 Days/The X-Files/Stargate SG-1 crossover called "Sex, Lies, & Conspiracy Theories." I begins with Dana Scully meeting with Senator Kinsey. They are both killed when his limo explodes. The NSA sends Frank Parker back in time to save Senator Kinsey, also saving Scully in the process. There's some romantic sparkage between Parker & Scully. Olga Vukavitch notices this and starts flirting with Fox Mulder to try to make Parker jealous. Meanwhile, Mulder & the Lone Gunmen investigate the mysterious Project Backstep and try to discover who Parker works for. After some rediculousness involving a sexy Australian assassin that tries to seduce Parker; Parker, Mulder, & Scully realize that there's a lot more going on than they thought. The three of them decide to team up, along with Olga & Nathan Ramsay. Their investigations eventually take them to the Cheyenne Mountain Complex in Colorado, where they have a conference with General Hammond. At some point, Col. O'Neill wanders in and exchanges a lot of bad jokes with Parker & Mulder while Olga, Scully, Ramsay, & General Hammond roll their eyes.
Not SF/F, but I'd love to see a Conviction/Law & Order crossover where Billy Desmond & Paul Robinette find themselves on opposite sides of a racially charged murder case. Since Robinette seems to think that every black defendant can use institutional racism as a mitigating circumstance while Desmond was always trying to distance himself from black political issues, I think the explosion here would be electrifying!
I also dig the BSG/Space Above and Beyond crossover. I'd have to think about this a little more...
Something i'd really like to see is Fox Mulder and Dana Scully on CSI or Fringe.
