Oh- and there was something about indexed palettes. Sorry, it's been a while.

GS .pcx files must be paletted. The first colour indexed will be transparent in the game.
Some video cards have issues with colours that have all RGB values lower than 10.
A colour like R8, G2, B1 might end up being transparent in-game, while something like R12, G1, B0 should be okay.
WB/Gurney’s 3dzStudio can be a valuable aid when working with textures, provided that you have the proper .3dz model. Many, but not all, of the .3db models used in Gunship! have unused .3dz analogs in the Gunship\Data\3dz folder that you can work with. Unfortunately, none of the hi-res helos (including the Blackhawk and the Hip) have .3dz versions.
If you can find the correct .3dz file for your texture, you can view (and change) how the wireframe is mapped in 3dzStudio. Makes texture editing a hell of a lot easier, imo. If your texture dimensions aren’t square, you’ll have to make them so before using the Studio. Some nVidia cards don't like anything mapped to coordinates 0x, 0y, 255x, or 255y. Just something to keep in mind if you're willing to remap stuff.
3dzStudio sometimes isn’t truly WYSIWYG. You might have a small number of elements’ mapping coordinates off by a pixel compared to what you see in-game.
If you do change mapping coordinates, you’ll have to convert your new .3dz to a .3db. There’s a 3dzread.exe utility in your \Gunship!\Data\3dz folder that’ll do that for you. But don’t run it in there! There’s a few .3dbs in that folder that were created as “native“.3dbs (as opposed to those .3dbs that were converted from the .3dz format). Running 3dzread.exe in the \Gunship!\Data\3dz directory will batch convert all .3dzs to .3dbs and overwrite the “native” .3db files. If I were you, I’d Cut&Paste that utility into another folder if you plan on ever using it.
Now, if you’ll excuse me, I’ll return to watching the Penguins beat up on the ‘Canes.
Good luck!
Oh, yeah, there is another MicroProse utility in your 3dz folder that can tell you which .3dz goes with which texture. I think fng2k has the relevant information available somewhere on his site.