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What game references have you found?

My list (of obvious stuff) so far:
- 5 corpses throughout the game (Caleb, Lo Wang, Serious Sam, Duke Nukem, Doomguy, Ranger),
- 2 shamblers revealed at the end of E2M11: Antarctica - Antarctic Anomaly are a reference to 2 barons of hell in E1M8: Phobos Anomaly in Doom,
- the layout of E4M11: Base - the Armory is mostly a copy of E1M1: the Slipgate Complex in Quake (the music track for that level is also named Quack).
the dead huskys behind the fences in the arctic station are a reference to the original movie "the thing" (like the whole layout and the enemy "thing")