Quite a Meta-Shout-Out, considering Edward Norton was the star of both movies.
The Naked Gun: The Imagine Spot of Green Goblin defeating all the brainwashed superheroes was a straight homage to the opening sequence of the first The Naked Gun movie where Frank Drebin beat up all of America's enemies in Beirut.
Wolverine: You hate Mutants! You're an anti-Mutite! Superman: I am not an "anti-Mutite"! Wolverine: Sure you are! Next you'll be sayin' we should have our own school! Superman: You do have your own school! Wolverine: That's it, bub! Keep pushin' it!