In the first mission, when you're boarding the ship, as you're about to go inside, gaz pulls out a shotgun and says "I like to keep this for close encounters", and in Aliens, when they're inside the base for the first time, and they have all their clips removed, one of the marines pulls out a shotgun and says the same line.
There's also a LT Vasquez in Aliens and CoD4.
Anyone noticed any more references?