I'd use them but not make it clear what they were. Giving creatures names ruins their mystique, and certainly the terror of "body horror." Having something burst out of someone's chest might be too iconic; encountering the eggs without any other context would certainly surprise someone even if they saw the movies.
I've recently based nearly all my d20 Modern scenarios on movie scripts, by taking the raw material of a printed scenario and then finding a movie script that is similar. This isn't very hard to do at all (a good or bad thing, depending on your perspective of scenario authors).
I have a big plan, actually, to use my Horrorclix Alien Queen along with the aliens in the scenario "The Source and the End" replacing the weird little mutant critters with aliens and the "source" with the queen. It should be suitably horrible.
The key is 1) not to tell the players what you're doing, and 2) tweak the monster enough so that it's presented differently. Make the Aliens read, or call them Thaliens, or whatever, and everything changes.
The other challenge is that pictures can make or break a scene. Just showing players an ALien will immediately give the point away. Describing it however is a different story.
Or you could just steal any one of the d20 variants that are already out there, several of which are in the 3.5 Monster Manuals.
P.S. Your counters are cool!
