Alien, Predator, Stormtroopers, Cthulhu, Joker and more released from the evil side. Some of the cameos were just outright obscure. I think they let their entire staff toss in random characters. The V on Wario's hat is a good sign they didn't ask permission to use anyone though.
Joker was based on Heath Ledger's "Dark Knight" makeup and not the comics which might make him easy to miss.
The scene where Manbearpig leaves the portal was taken from Doom 3.
I'll be disappointed of Dr. Greg House isn't in part 3.