I used the following program in my Team Fortress 2 Mods. It is not a free program but it is worth the investment if the need is really there.
People have asked me how I made those skins, it's a blend of real-world photography, GIMP knowhow, and this program here.
Find more of my work through these links:
Find me using these links, and please feel free to contact me with questions or comments about any of my work!