1. Grab the Softimage XSI Mod Tool 6.01. It's FREE (DON'T GET SOFTIMAGE 7.5! you have to pay for that version). Now you have a modeling software. Wings3D is also good (and open-source); however XSI Mod Tool is required for hardpointing (adding particle effect points) and UV-mapping the model.
2. Grab an image-manipulation program, like GIMP, Adobe PhotoShop, or Jasc Paint Shop Pro. GIMP is the best one, as it is open-source; grab the dds plug-in for GIMP as well (you'll also need to use it on 32-bit; the plug-in crashes on 64-bit).
3. Make your model; UV it, create the skin, export it using XSI, convert it with the ConvertXSI utility in the Forge Tools (also useful for the docs in it).
Also, I recommend grabbing the Dekhranic Mod Tool GUI. Search for it on the forums. I recommend it as it has a GUI utility for using the ConvertXSI program, so you don't have to run it as a command-line utility. Plus, it's used to TXT the binary files for the game, allowing you to make the coding for a ship.
