There's Photoshop, but then again that costs money (unless you have קומבינו& #1514;
). Though for some reason I've been unable to save .tga files with an alpha channel (it automatically turns into 100% "visible", so it works for converting maps, but not to add some invisibility to the mix)
You can just wander the vast exapnses of the internet for any freeware that supports .tga and alpha support.
*wonders if he can make a little program that will fix alpha-troubled maps*
*realizes he can't write programs to manipulate *.tga files*
Endoperez 
Agrajag 
Re: DomII maps in Dom3, and fixing that Alpha chan
Threaded Mode