I'm pretty sure you can, and I've been thinking of doing it myself.
You basicly make a movie, save it as a .avi or other common format (sorry, no Windows Movie Maker, that peice of crap only saves in .wmv, a proprietary format).
You download and install the bink video tools, then covert it to a bink file and replace the game movies with it.
You can replace the Activision logo (do it!), the Taldren logo (no, be nice to taldren), the Paramount logo (depends how much you like Enterprise), or the opening Movie.
You can also replace (or play if you want to see them!) the ending movies without having to beat the game.