Oh man, Pardus... Thought I was the only one in the history of the internet who remembered that one! Was beginning to wonder if I imagined the whole thing. Gimme a Scorp with x2 BSAs, x2 Viral Glands, Huge shield and x6 Pardus armor... hold full of bots, drugs, and 5600 APs ready to burn. Good times.
Another totally different game had fantastic weapons customization: Aurora. http://aurora2.pentarch.org/ Not only can you choose between kinetic weapons, energy/beam weapons, and missiles, but each one of those options has multiple layers of design and customization. It's a near perfect build your own gun system; more detailed even than From the Depths. Of course, Aurora is 2D and has no graphics to speak of... oh well.