You can use PSP to make ship graphics. I'm quite sure it can output 32-bit (RGBA) .tga files as it's a very common file format. However, I have not used it myself.
OK... when I tried doing the graphics a few days ago, I could make it but then when I saved it as a .tga file, it would merge all the layers. Perhaps I was doing it wrong. I'll try it again.
I keep putting that off... Maybe next month if I remember (We're trying to submit something to IGF with the deadline being 9/30, and I'm shipping another game at work that's kept me really busy for the last year)
Hmm, I was wondering if it's possible to make completely invisible spaceships by simply making a completely black/blank alpha channel on the ship graphics. Maybe Fingers could help? I'll try it soon anyway.
Well, i don't mod all that much but the problem i see is that enemy ships wouldnt know its invisible so if you have a three way battle the ai would just attack it.
I wonder what would happen once the shields are down and the missiles are trying to crash into the solid part of the hull. If they can never hit white on the alpha layer, I'm not sure they'd ever be able to hit. They might be able to knock down shields, but maybe not finish the ship off.