In the first level (Time To Split) when Cortze is holding off the Time Splitters with the gun emplacement one of the soldiers says "They're coming out of the walls! They're coming out of the goddamn walls!" A quote from from "Aliens".

When you select the Gingerbread man for multiplayer he says "Bite my crunchy brown ass." A direct reference to Futurama's Bender and his catch phrase "Bite my shiny metal ass."

In the eighth level (You Genius, U-Genix), after you get the disguise, Amy says "Remember, your name is Gordon now. Lead the way, doctor." This is a reference to Half-Life's main character Doctor Gordon Freeman.

In the fourth level (The Khallos Express) after the Khallos uses the poison gas you can control his pet cat.

A drunk character appears in every level of the game aside from he first and last.