The Oblask Dam in the Siberia level is a shout out to the Bylemore Dam level of GoldenEye. 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 Neo Tokyo level takes its name from AKIRA, but is intended as a homage to Blade Runner. It has the floating cars, the asian influenced culture, and the the incessant 'Cross Now' from the street signs.
It also pays homage to Neuromancer, as the protagonist of the level, Ghost, is similar to the character Case. His gallery description mentions an AI Core and lists his occupation as a "cyberjock."
In You Genius, U-Genix, Cortez obtains the ID card of a scientist named Gordon.
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!" and "They're coming outta the walls! They're coming outta the goddamn walls!".