Red UFOs drop a life fragment upon being destroyed, as well as when they're filled to max.
Green UFOs drop a bomb fragment when destroyed, and an entire bomb (!) when filled up.
Blue UFOs give a massive score multiplier.
Rainbow UFOs give a score multiplier, in addition to converting point items to power items (and vice versa, I believe; useful for quickly gaining power). They also release a UFO upon both being filled and being destroyed, based on what the last color UFO was that you used to make it.