A combination of The GIMP and Adobe Photoshop CS4. I basically take an artwork that has transparency, and covert it into a .tga image with The GIMP. I then open the .tga file in Photoshop CS4, and convert it into a .png file. TarGA transparency is handled differently than PNG transparency with Photoshop CS4, utilizing alpha layers for transparency, instead of a checkered background.
By removing the .png file's alpha layer, that enables me to fully cover any parts that would be semi-transparent with The GIMP. And once I've made the palette swaps, I then reopen the .png files with Photoshop CS4, implement the .tga file's alpha layer onto each .png image, and then convert them all into .tga images with an alpha layer.
To finish off, I then use The GIMP to load all the .tga images onto one image, and then align them with each other, usually being a 3x2 (3 images wide, and 2 images tall) setup. That very image is saved as a .png file, designed for uploading.