Wings3d is a 3d modeling program grab it here:
http://www.wings3d.com/
DDS converter, converts .dds files to .tga's to be painted:
http://files.filefront.com/DDS+Conve.../fileinfo.html
HEX editor, changes crash dive depths, 3d models, ship wakes and everything else:
http://www.softcircuits.com/cygnus/fe/
Deep Paint 2.0 allows you to edit the ship skin, forgot link, its kinda hard to find.