The Last of Us - There's a few useful women and a few are actually good characters. They don't have the need to do hyper-masculine things either.
Chrono Trigger - Female cast are developed and useful characters. They have both serious and silly sides to them.
Tales of Phantasia - All the girls are awesome, especially Arche. Just a fun character.
Metal Gear Solid - Sniper Wolf, Meryl, Mei Ling, Naomi
Tomb Raider (Remake) - Laura Croft actually becomes a very good character. A huge transition from being tits and ass.
The Walking Dead - Unsure if these counts as games, but Clementine is not bad. Nearly every other female character is a psycho though.
Persona 4 - Chie was enjoyable.
Mass Effect - Most of the female cast is pretty decent.
Resident Evil - Rebecca is a sweetheart and made of love. Jill is very good in the original games. While things eventually get really weird, the female cast isn't to blame.