Junk Yard us full of references - TAF, AFM and CFTBL in the Time Machine, Who Dunnit, Mousin Around and possibly Doctor Who and TOTAN in the art and sound references to IJ, among others.

It was originally concieved as a game made up of "leftover" ramps and devices from other games and, while the physical game is all original, they kept a lot of the references to the old games.

I was playing Deadpool today and got my first "Who are you? Keith Elwin?"
Not a reference to a specific game, but still a fun inside joke.

Tonight during one of the Multiballs on Deadpool, I swear he started singing the Bride of Pinbot’s opera aria.