My favorite character by the end of season three was Murphy. Murphy! Never would have believed that in earlier seasons. Never underestimate the power of a witty one-liner, consistent characterisation and believable character growth. (and all your previous favorites behaving completely out of character)
Clarke annoyed me this season. Yes, she stayed with the grounders, but she could have spent a bit longer making others understand why she was doing it and smoothed over some things (but I guess that wouldn't have served where they wanted to take the plot). She seemed very primadonna to me this season and only started acting in ways I could identify with towards the end.
I was fine with Bellamy season one and season two. While Bob Morley continues to be a favorite of mine, Bellamy was just stupid too many times this season for reasons that only served a plotline. Once all the characters reunited he started getting better and motivations became clearer and some of the damage was repaired, but still... I do think relying on the 30 second girlfriend with whom he had no chemistry for motivation was a mistake. I couldn't understand why he was following Kane one minute, with almost a fatherly vibe, and then wouldn't listen to him the next. Still, things were getting much better towards the end of the season.