My 3 favorite characters for all my fandoms. What I consider a fandom of mine is entirely arbitrary - I'm not including Harry Potter because I find myself bored by it at this point, but I'm including fandoms that have only one or two fics, and no discussions, because I'm finicky like that.
Oz
1. Ryan O'Reily
2. Miguel Alvarez
3. Jazz Hoyt/Liam Meaney (tie, not ship)
SVU
1. Brian Cassidy
2. Casey Novak
3. John Munch
Criminal Intent
1. James Deakins
2. Bobby Goren
3. Alex Eames
CSI
1. David Hodges
2. Greg Sanders
3. Bobby Dawson
CSI NY
1. Sheldon Hawkes
2. Danny Messer
3. Don Flack
NCIS
1. Tony DiNozzo
2. Abby Scuito
3. Tim McGee
Veronica Mars
1. Cassidy Casablancas
2. Leo D'Amato
3. Don Lamb
Crossing Jordan
1. Matt Seely
2. Bug
3. JD Pollack
Numb3rs
1. Colby Granger
2. Don Eppes
3. Larry Fleinhardt
Rescue Me
1. Johnny Gavin
2. Mike Silletti
3. Sean Garrity
21 Jump Street
1. Doug Penhall
2. Dennis Booker
3. Adam Fuller
Dark Angel
1. Alec
2. Logan Cale
3. Sketchy/Normal (tie, not ship, although I do ship them)
In Justice
1. Charles Conti
2.
3. David Swain
Wanted
1. Eddie Drake
2. Jimmy McGloin
3. Rodney Gronbeck
Wonderfalls
1. Aaron Tyler
2. Jaye Tyler
3. ...Aaron Tyler again. (I love him!)
X-Men (movie)
1. St. John Allerdyce
2. Scott Summers
3. Bobby Drake
X-Men (evo)
1. Jamie Madrox
2. Pietro Maximoff
3. Scott Summers
X-Files
1. Fox Mulder
2. Alex Krycek
3. Dana Scully
Dark Lord of Derkholm/Year of the Griffin
1. Flury
2. Blade
3. Felim
Chrestomanci Quartet
1. Charles Morgan
2. Cat
3. Dan Smith