Toughie as I'm not a big fan of the female characters strangely enough. I think I'll have to go with Claire. She's an important character all the way through the series, especially her relationship with Kate. She gets some really interesting flash-backs and is central to the great unanswered question surrounding the importance of Aaron (if he's important at all). Also she gets Charlie so she's bloody lucky. Oh and she goes fucking mental. Squirrel Baby anyone?!
Other than that I think Libby is a good character, once again she's mental and very sweet. Ana Lucia is pretty hot so she'd rank high too. Alex as well, especially in the flash-sideways.