Batman has his own stories but now and then runs into Superman. In Today's Speak Up on Kotaku commenter Aikage imagines a video game universe filled with countless games linked by a single continuity. What an Oddworld idea.
Video games need to take a cue from comic books.
It'd be great if instead of endless sequels, we got games in a similar vein, in the same "universe" but different main characters. The closest thing to this I can think of was Dragon Age 2 compared to Dragon Age: Origins. Different main character but the game takes place in the same universe.
If this doesn't appeal to you think of it this way, You're playing Uncharted and one of the treasures you're after is something that was being created during your play through of Assassin's Creed. In comic books the effects of one comic frequently will be mentioned, or have an impact in another comic. This sort of interrelatedness among the issues leads to awesome things like...the Avengers movie! (hopefully).
Anyway, if you could design some video game crossovers regardless of publisher/developer who would you have meet?