I haven't gotten through enough to qualify for a really good answer on this, but I have many to get to: I played ACE Academy most recently, and it was pretty good. Favorite? I don't know since I've only been through a few of them - just the first one that came to mind since it was recent.

Katawa Shoujo

GO GO NIPPON

Didn't play many :P

What Superfabs said.

Thank you very much for the game!