Good paint app for game design?

I’m working on a project that I need to have complete control of each color in an image’s 256 color palette. It’s basically a simulation game using DirectX, and in order to allow transparency in bitmaps, I have to be able to “move” a particular color to color palette position #1. I’ve got an ancient version of Photoshop (v 3) and Gimp, but manipulating the color palette is a pain with either one. What do you folks that work on games use for this? Are there any open source or free apps I should try?


what about Dogwaffle?