Paul could answer better... I think it is (or was) Lightwave 3D or some such thing.
Basically with these trailers, I go to Paul with a shot list culled from a script, or a script-in-progress, a specific as I can get in terms of look and direction. Paul takes that and crafts a ton of shots which he uploads to our FTP. I grab 'em and edit them, usually to music of someone else's suggestion (Jay often picks out our trailer music), although this time, I also chose the music. Henrik has polished off our trailers in the past with top-notch audio mixing, sound effects, and so forth.
It's an interesting process, a truly global collaboration as, outside of Jay and myself, everyone else is across the pond. We've also used the likes of Craig McCue, Cynthia Dusenberry, and Jaron Hatch for our voice acting. (Craig is, in fact, doing a voice for this trailer, along with myself and some others.)
The process has evolved from showing simple, ship-based clips from our episodes (usually the Enterprise, either in battle or doing something interestig) to this, which will be sort of the culmination of all the CG stuff we've ever done. At just under five minutes, it's going to be a big trailer. I fear Paul's computer may not like him much after all the hours of rendering.