Of course, the better (i.e. more $$$ you spend) graphics editing software you use, the better your skin is going to turn out. I use corelPHOTO-PAINT 7.0 for my editing, which works pretty good, and was quite a bargain, but (I know from experience) if you want to draw some pretty good pics to use for skins, you can download demos of Photoshop with just about all doodads enabled except for save - so you just use a shareware screen capture util.
The first step in making a good mat is to of course get a mat2bmp type utility. I recomend MatMaster, by Peter Klassen and the Code Alliance. Choose your 3do (I'm fond of the tusken model myself) and take a look (open it up in notepad) at what textures make up the model (you can find more information on this in October's issue of Darkness Falls). You may have already done all this, and know what resolutions, which surface is what, etc., to make your skin. If not, find and extract all these MATs with ConMan, also by the Code Alliance, and then convert them to BMPs (when using MatMaster, you can go ahead and delete all the MTM files when working with model textures - and you may want to rename the BMPs).
Open the BMP(s) into your editor of choice, and convert the palette (this procedure may vary depending on the editor) to a custom set. Save this set as JK.cpl or whatever, and hit cancel/ok. You will need this palette later. Convert the BMP to 24-bit color, or create a new blank image the same size (it is easier to use the original BMP as a template).
Now you just draw your pic, and convert it to that palette you saved.
However, it's usually harder than that. I have a method I use to make my pics that turns out very good when making smoothed organic-surfaces like kyle's head or a giant cheese log. Here's an example, a JiB skin (this was the first skin I made, and it doesn't come out quite so well in the end, when placed on the model with all other textures, but alone it illustrates my points quite nicely).
-Kyle's head- After saving it's palette and converting it to 24-bit, I then desaturated it (made it black and white).
-Kyle's [grayscale] head- Simple enough. now comes the real editing, the skill you put into your MAT. Smoothing out highlights and changing the hair with a smearing tool, then making parts darker (black for the parts of his face that are black, white for the parts that are [whatever color you are going to make them], you make your face.
-Kyle's [revised] head-
Well, it comes from experience. Actually, it wasn't all that hard. Remember to use adding and subtracting brushes. Next step (we're almost done!) is to make it COLORed - just pick paint colors for skin, lips, whatever, and color over a duplicate of your pic. Very Easy.
-Kyle's [colored] head-
Hehe . . . looks pretty gross, huh? Multiply (depending on editor, probably something like Image>>>Calculations) this and your grayscale head together - voila'! Beautiful.
-Kyle's [beautiful!] head-
Done . . . for all practical purpouses. Convert this to the JK palette and convert it to a MAT and put it in your 3DO . . .
Isn't that much better? And more Jedi-in-Black like, too.
And this can be done not only with plain old guy's faces, but aliens and mutant brains and whatever also (Not the Terminator, that one's claimed by Yours Truly). Oops! I forgot to add those Ray-Bans . . . oh well, my problem, not yours.