The Oblask Dam in the Siberia level of 2 is a shout out to the Bylemore Dam level of GoldenEye 64. It uses a very similar dam, camera movement in the intro and a lot of the same noises. Hardly surprising given that some of that game's devs became Free Radical Design members.
The Chicago level features a bar called O'Leary's.
Also In You Genius, U-Genix, A fleeing guard cries "Game over man, game over!" A reference to the film Aliens. An earlier reference to Aliens occurs in "Time To Split", when a space marine is heard saying, "Shoot anything with teeth bigger than its face".