Im playing Muv-Luv at the moment. Can't really comment on the story yet, but at least it's really well made, especially considering it's from 2004.
Also I thought Kono Oozora ni Tsubasa wo Hirogete is awesome in all aspects, but many people dislike some of the routes.
Also I've heard very good things about Little Busters, but I didn't play it because I didn't like the sprites, and the system didn't get along with me.