If there is any one subject I have gamed more then any other, it is Star Trek. I've run a least one game using every edition and version of the subject put to rules and I have learned a great many things. Please keep in mind this subject is near and dear to me so I may rant a wee bit. You have been warned.
GURPS is way too complex a system for the fast paced, cinematic feel of the television shows and movies. While the point based system allows for many interesting options, it just doesn't lend itself to a game with a Star Trek feel. Likewise D20 does little to give you the impression it was made for Trek, since it wasn't. Also, D20 Race/Class systems, even those of a SAGA/D20 Modern ilk, don't seem to allow for easy adaption to the possibilities inherent in the Star Trek universe.
The Decipher Star Trek game sadly feels very D20ish to me, with 'feat-like' abilities and trying to shoehorn Trek character types into class-like professions that don't easily translate older characters or those who have transfered to Starfleet from some other field or vice-versa. In addition, the CODA system always screamed, "We made this because we couldn't use Last Unicorn's ICON system. Isn't it similar?" Yes, it's similar. That's doesn't mean it works quite as well.
The ICON system version by Last Unicorn Games is perhaps the best merger of detail and flexibility I have ever seen for Star Trek gaming. It was well supported by people who were real Star trek fans and is currently kept alive on the internet by some very talented and creative people. I have the pleasure of playtesting the game and working with several true kings of the industry on one of the sourcebooks. I never had so much fun and I got paid to create Star Trek characters. Nirvana. I have run about a half dozen campaigns with this system and it is capable of handling any era, level of advancement and style of play from Starfleet to civilian.
The FASA system is a bit dated, a bit limited and totally, classically awesome. I grew up on that game as much as I grew up on Star Trek itself. I still play it occaisionally out of a love of nostalgia. It was the first game I bought with my own money and still a fan favorite of mine.
If you need any resources or have any questions please let me know. Good luck and godspeed!
AD