Personally I'm fairly new to the genre and I have only played through a couple of really good ones to date, but for me grisaia no kajitsu (or rather "the Fruit of Grisaia" which I know it as) is one of the better ones. For me though it's the fact that a lot of the behaviour in the VN seems very realistic and goes in to somewhat dark themes at times which really makes me care for the characters somewhat.
I have't finished all the routes yet, but so far I would at the very least put it up among the better ones I have played. That may change in time though (especially since my current mastery of the Japanese language is severly lackluster which hinders me from reading a lot of them), but it really is a well written story.