So many references:
Root Beer Tapper
Gears of War
and many many more
But my absolute favorite reference besides the KONAMI CODE!!!!! was...well...lets just say it involves METAL GEAR SOLID!
Oh and do yourself a favor, when the credits start rolling just sit and enjoy what you are about to see. One of the best credits I've ever seen.
Definitely one of the best movies of the year and one of the best animated films of all-time.
Oh and that short before the film, Paperman? Disney, you made me fall in love. Amazing short and honestly better than anything Pixar has ever done. Not only will Wreck-It Ralph be winning best animated film this year, but I would be shocked if Paperman didn't win best animated short.
Edit: Forgot to mention, but I said to watch the credit...I also meant stay to the very end. It isn't Iron Man level of "HOLY SHIT", but it was pretty awesome. All I'll say that it is one of the most famous kill screens besides Donkey Kong.
Edit: Also, for anyone who isn't into video games or don't want the whole movie to be "oh look! a COD reference!", it has an amazing story with a lot of heart, great voice acting, and not only great heroes, but a truly great villain. Btw, Alan Tudyk does the voice of the villain (won't spoil who it is since it doesn't sound like Alan Tudyk and its a plot twist), but its awesome. A good portion of the movie takes place in a Karting game that has no real references outside of probably Strawberry Shortcake and candy.
Amazing film, one of the best of 2012. Go see it (even if you don't play video games).