Well, it might have been even more interesting if we'd left out ALL scifi characters - not just Trek characters. But in any case, there is only one Trek character who would make my top 5 anyway, and that would be Ben Sisko (big surprise).
But leaving out Star Trek, what I decided to do was make a list of several of my favorites, and then highlight the top 5. It's just too hard any other way.
Londo Mollari (Babylon 5)
Sayid Jarrah (LOST)*
Desmond Hume (LOST)
James "Sawyer" Ford (LOST)
Richard Alpert (LOST) (expected favorite, after we find out that he really runs this shit!

)
Jim Rockford (The Rockford Files)
Hawkeye Pierce (M*A*S*H)*
Frank Burns (M*A*S*H)
Tony Soprano (The Sopranos)
George Costanza (and his Festivus-celebrating parents) (Seinfeld)
Lilly Rush (Cold Case)
Jack O'Neill (Stargate SG-1)
John Sheppard (Stargate: Atlantis)
Mal Reynolds (Firefly)
Angel (Buffy/Angel)
Spike (Buffy/Angel)
Fox Mulder (The X-Files)*
Charles Ingalls (Little House on the Prairie)
Jethro Gibbs (NCIS)
Tony DiNozzo (NCIS)
Frank Pembleton (Homicide: LOTS)
Richard Channing (Falcon Crest)*
Angela Channing (Falcon Crest)
Dr. Addison Montgomery (Grey's Anatomy - not so much in Private Practice though)
Dr. Derek Sheperd (Grey's Anatomy)
Sen./President David Palmer (24)
Jack Bauer (24)
Christine Cagney (Cagney & Lacey)*
Denny Crane (Boston Legal) - tough pick between him and Alan though
Alan Shore (Boston Legal)* - tough pick between him and Denny though
Jaye Tyler (Wonderfalls)*
John Crichton (Farscape)
Aeryn Sun (Farscape)
Norm! (Cheers)
Lex Luthor (Smallville)
The Doctor (Tennant only) (Doctor Who)
Lee Adama (nuBSG)
Kara Thrace (nuBSG)
Saul Tigh (nuBSG)
* denotes strong runner-up