Lots, especially the "original" games.
- Kid Radd 2 is Super Mario Bros. 2, and Mofo is clearly EarthBound.
- Final Legacy. So obvious it hurts.
- And the passcode for the chimerization chamber is 8675309.
- A Castlevania: Symphony of the Night shout-out: "What is a sprite? A miserable pile of pixels!"
- The MST episode is called Deep 13.
- One comic has Radd turning Captain QC into a clone of himself.
- This is clearly a MacGyver parody.
- Food is powerups from various games.