It's not reference to anything, but Misused Apostrophe's made me laugh.

Oh, also Bit Trip Runner. Well, maybe it doesn't count as a reference when the game itself is there (you can play it in the arcade), but it's there nevertheless.

Also, Minecraft. I'm surprised that hasn't been mentioned yet.

Boy, it's been ages since I last updated this list. I've added the following references:

Gargoyle's Quest
Doki Doki Panic
Jackal
X-COM
Scrap Metal
Leisure Suit Larry
Little Nemo: The Dream Master
Pac-Man
Ms. Pac-Man
Urban Champion
Q*bert

MacGyver
Tenacious D
Nintendo Power
Spiderman
E.T.
Last Action Hero

Thanks to everyone who pointed out the ones that I missed!

PS: To everyone who said I missed Super Meat Boy, BIt Trip Runner and Minecraft, I don't count those because they are direct cameos, not just references. I made that very clear in the first post.

Added Magnum P.I. and The Incredible Machine to the list.

I just found a VirtualBoy version of Super Meat Boy, and spent half an hour playing that alone. Next time, I'm going to do it with 3D glasses.