Ianto Jones from Torchwood, definitely. Oh, Ianto, ever in my heart... Also love Stuart from the original UK Queer as Folk because Aiden Gillen. I also admit a soft spot for Kurt from Glee. I think he's a fantastic character, and very well rounded.
Can't help but notice that no one seems to have mentioned any female characters (I just skimmed, though)... Is this the kind of environment where we differentiate between gay and lesbian, I wonder...? Either way, I feel the need to mention Charlie from Supernatural, played by the awesome and very, very hot nerd icon Felicia Day.