I'm guessing some of you have already noticed, but you can open up the image files for the your ships, the alien ships, and other things and edit them on paint to make them whatever color you'd like. You just have to replace the original. (make sure you back it up) Mine has amazingly bright fun colors now.
You can probably do this with other games.
I've also noticed in alien aggressors that if you want to edit bullet colors, you have to change the coding. It isn't very hard to find, but be really careful if you do anything.
EDIT: I've also been playing with the audio tracks. It's pretty neat. Soon enough I should have a Daft Punk edition of AA uploaded.