In Reel Steel, Wolverine is friends with Falcon and gets bullied by the Blob.
In The Spirit, a comic movie as well, both Nick Fury and Black Widow are present, but are now evil. Also, Ghost Rider's girlfriend and Lucille form Sin City pop in.
Demolition Man has Judge Dredd fighting Blade.
The new King Kong prequel coming out in a few years only has three cast members so far: original movie Batman, Loki, and J J Jameson.
In Juno, JJ Jameson has Kitty Pryde as a daughter who befriends Elektra.
In Inception, Kitty Pryde, Robin, and Bane team up against the Scarecrow.
I'm surprised no one (besides me) has mentioned American Hustle yet, either: Rocket Raccoon, Mystique, and Batman in the same film.