Alright. I decided to ask all of you this question because I really can't decide myself, (well, that and Clannad is my favorite series so).
I don't know if anyone else experienced this while watching Clannad and Clannad After Story but I could never make up my mind on my favorite female character. During Clannad, Kotomi was instantly my favorite. She was just so adorable and her backstory really got to me. Kyou and Tomoyo tied for second, and I didn't think too much of Nagisa.
However, once After Story aired, my opinions began to waver, and I really grew to love Nagisa as a character.
I also adored Fuko and Ushio throughout, and Sanae is definitely a milf for me.
Once I'm done playing Fate/Stay Night, I will be playing the visual novel, and who knows? Maybe my mind will be changed once again.