Alien vs Predator 3. After the Aliens have ravaged the Earth and created a huge infestation, humanity creates Terminators/Skynet to fight get rid of the alien menace. Meanwhile, in Detroit with the end of OCP Robocop takes on the mantle of ‘The Punisher’, to fight the alien scourge.
Robocop/Punisher of course is our hero.
Mr Bean the Witch and the Wardrobe.
Robocop vs Terminator has been written. It was pretty good, too.
Indiana Jones and the Chamber of Secrets
Titanic Carrie.
After a lifetime of abuse at the hands of her gold digging mother, Carrie can’t take it anymore when her pervert forced-marriage fiancé beats up the first man to ever show her kindness.
New, Improved Team America.
Peter Parker and Clark Kent notice that the Team has essentially the same goals as they do, with better paychecks, so they sign up.
N.Y.P.D. Blue’s Clues:
Fancy: That is not a pretty corpse.
Medavoy: This poor slob was sliced, diced and chopped.
Sipowicz: You want we should haul in Ron Popeil?
Blue: RRrrewwrr–ehwm?
Steve: Hey guys, look! Blue just brought us a clue!
Fancy: What the @#%& is that?
Steve: It’s an orange triangle!
Blue: erk–ooooo!!!
Medavoy: And what the &*))&^$%^&)&^%% %^&(^!@ are we supposed to make of that?
Steve: I don’t know.
Blue: oughhhhrrmmm–mwfewwroo!
Steve: That’s a great idea, Blue! Let’s go sit in the…thinking chair.
Sipowicz: Yeah, yeah, that’s great. You go sit in your thinking chair…somewhere else. God, you’re twice as annoying as Caruso was.
It was damned good…especially the ending. I about shit my pants laughing when the T rex stepped on the robot dog.
House treats Bertie Wooster 
Star Trek-Wars, of course. The Federation begins exploring an uncharted part of the galaxy and stumbles across the Empire (naturally, they’d throw in their lot with the Rebellion).
Which Trek species would join up with the Empire (Romulans, Ferengi, and Kardassians, of course – maybe Klingons). Which Trek characters would learn the ways of the force and become Jedi knights (Wesley Crusher’s a shoe-in). How many Galaxy-class starships can an Imperial Star Destroyer take on at once? Etc.
I just came across this again today, and although it’s pretty old, it’s quite appropriate for this thread: The Ultimate Battle of Ultimate Destiny.
I know both shows are ended but I always thought it would be fun if Tony Soprano’s crew took a road trip to Baltimore and tangled with the Barksdales or Marlon/Chris/Snoop.