varsaigen: Are you going to use this texture in retail FreeSpace 2 or FS2Open?
Because for retail-compatible stuff, you need a PCX texture. If you use FS2Open (which is in most cases advisable due to better compatibility for new PC's, loads of new features and so forth), then DDS is basically the preferred format for textures, although the game can use TGA's as well. For the duration of testing the textures it's generally best to use uncompressed, lossless format - in case of FS2_Open, it'd be TGA - and convert it to DDS when you're done with it.
Also, I've found that GIMP is pretty much sufficient for the graphics work related to FS2_Open, although IrfanView is really good for batch converting a lot of files... and I tend to prefer NVidia's DDS tools (nvDXT command line utility) for converting files from TGA to DDS, but that's just my preference, any way is acceptable as long as the end result looks good. GIMP/Photoshop DDS plugins do good work too, it's more a matter of choice as far as I know.