In the Monorail LCD screen they hid animated text that said "Preparing to destroy Disneyland!" with flashing missiles.
Donald Duck was also never supposed to appear in the window in Central Plaza - Disney originally refused to include any classic characters because they believed they weren't popular enough. Someone from Sulake thought otherwise and put him into the game last minute without telling anyone!
There's probably a bunch more inside jokes hidden in the game, just never found them yet.