I have way too many to name, but some off the top of my head:
One of my favorites (up until 3rd Birthday at least. Please, let's not discuss that horrible game.) because she was a strong female lead when they were just getting big in games. Also, she seemed pretty caring, which made her more human compared to most "tough" girls.
White Knight Leo
Lunar 2: Eternal Blue / Lunar 2: Eternal Blue Complete
I don't know why I love him really. I think it's his sense of justice, which is wholy his character. Even when everything he's served turns against him, he still does the right thing not because he was ordered to.
Aerith Gainsborough (oh god, don't flame me)
Final Fantasy VII / Crisis Core
Aeris/Aerith always held a sentimental spot for me (for reasons everyone knows) and like Aya, she was a real sweetheart who had a backbone.
Squall and Tidus are some of my other favorites, just because I really like their personalities.