In TBP or Babylon 5 in general?
In TBP, has to be the Aurora Star Fury - It just looks gorgeous, and so similar to the TV versions.
The updates to the pulse cannons just make it even cooler!
Nail gets a second place - It's a nice ship, also looks like it's TV-counterpart. The best thing about it is the fighter beams - They look and sound freakin' awesome, even the barrel flash is a neat touch!
I wanted to say the Thunderbolt, but to me it looks kinda ugly and not that much like the TV version for some reason...
In terms of flying, the Badger. I can't have an Ares so the Badger is the next best thing, and OHK'ing fighters with a spread of 60mm pulse cannon fire is always very satisfying

In the TV series... mmm... either Babylon 5 itself, or the EA Omega destroyers. The whole looks just screams "I'm Really F'ing hard, don't mess with me or I ram this particle beam up your exhaust port!"
My only regret is no one thought to mount heavy beams on the rotating section... would have been funny watching it cut big holes in other ships
