My favorite VNs should be CLANNAD, Rewrite, Grisaia Trilogy (although I have not finished Grisaia)
CLANNAD has many routes and different endings, but the developer built a good plot for each character, I can say that in Key didn't leave any route unfinished, all questions lead to an answer. Rewrite is a little bit too long, well, to be fair I will play it again someday.
I do not like Euphoria, School Days. Euphoria contains high sexual content and many disturbing scenes which far too hard to watch, about School Days, Dickoto is the cause. He should be killed a thousand times.