3D Studio Max
3DS Max is among the most popular 3d modelling tools within the community, together with trueSpace and Blender. Max's key advantages over TS are its much simpler interface and camera controls, as well as the preponderance of tutorials available on the Net. Volition built all of their in-game models in 3DS Max.
As professional quality software, Max is quite expensive, but a stripped down, free version, GMax can be downloaded for free, and models can be extracted via an .md3 exporter and conversion software such as Lithium Unwrap or Deep Exploration.