omrob has run a Warhammer Fantasy game with 3e dnd rules off and on for years now. Once WHFR 2e came out, though, we started a true WH campaign using the WH rules, and the dnd game went on hold.
I've run several "crossover" games where we mixed systems- some 2e dnd characters in my campaign went to the World of Darkness and had to deal with a vampire, for instance. We used the Storyteller system at the time for that session, but it wasn't a great mix.
I've played DC characters using Marvel rules, too, but that just barely counts- if that.
I've tried using 1e dnd as a baseline for sci fi games, including ones set in the Star Trek universe. Never did this one enough to really get a sense of how well it was working out, though.
Also, I recently ran a campaign arc for 3.5 that was set in a magical apocalypse, that was heavily influenced by (I don't quite want to say "based on") Gamma World. (The story hour describing the campaign arc starts
here.) Also, we had some GW characters come to Oerth back in the 1e days and get marrooned there. So we had some Gamma World with dnd rules.
In general, I love this kind of thing, but the Vampire crossover taught me to be careful to make sure that the systems support the same flavor and type of game.