Godai from Maison Ikkoku really got on my nerves. I wish he would just man up sometimes during the series and fix his relationship with Otanashi (SP?) but it would never happen. I guess if he would have, there wouldn't be much of a show, but it really got on my nerves and the end result was me not liking the show nearly as much as I would have, (however I still enjoyed it).
I personally liked Shinji from Evangelion. Don't get me wrong, I hate whiny characters as much as the next guy, however I felt it was justified by his situation. Not only that, since he was a reflection of Hideaki Anno (the creator), I felt his behavior was more real, therefor understandable. I think Shinji Ikari is the only whiny character that I could stand.
Naruto filler was crap, nuff said. Griffith from Berserk was a son of a gun for sure, but he was a guy that you'd love to hate, (after the series of course), and I love villains that do that to you, because that means they did their job well. He reminds me somewhat of Johan from Monster.
Nice topic, I like reading your guys' thoughts.