Yet again AND King Flippy for Aquaria Towers of Spyro 2. Listen to it and tell me it's not Boyd.
Orphaned Reference: Primal memories are a special reward for collecting all emotional baggage within one world, and show concept art pertaining to said world.
Tuckerization: A retroactive example: Tim Schafer's daughter Lili, who was born a few years after Psychonauts was released. Presumably Tim's fond of the name in general, but Lili-in-the-game now serves as a reference to real-life Lili.
What Could Have Been: The concept art for Gloria's Theatre shows much more detail than the actual level.
Waterloo World originally had a small, functioning strategy game that would be played rather than the comparatively simple missions you're given, but it was taken out because it was boring.