Subtle references to the Matrix
1. The level on Hero's Duty looked the dystopian surface of the real world.
2. The cy-bugs were like the sentinels and at the same time like Agent Smith, reproducing exponentially and threatening to taking over the computer generated environment.
3. Vanellope and King Candy's glitching revealing the blue code, similar to the Matrix's green code that Neo could see.
4. The characters without a game or "Going Turbo", very much like the renegade Matrix programs that hide in an alternative environment when they face deletion.
I'm sure there are others. Any more?