The cat. Normally Dogs and Cats in movies (And to an extent real life) react violently to robotic figures that move and act like humans ala Terminator. But this one when it meets Archer it looks at him curiously before affectionately licking his face, with Archer chuckling.
The Commandos mourning Nick Nitro, showing they're not complete sociopaths. Well, kind of. A little spoiled by their over-the-top blubbering, and Chip ripping out Nitro's processor - his brain - in order to form a base intelligence for the Gwendy-steins.
The scene where Irwin meets the Gorgonites, he goes from slightly impressed that his creations act like how he made them to be, to terrifyingly amazed that they are able to act like human beings. A rare good example of Gone Horribly Right.
Alan and Christy's Big Damn Kiss at the end of the movie. Extra points for the helicopter wind and Jerry Goldsmith's score.