I don't think I can be called a visual novel fan, only having played the most popular ones. But these most popular ones were all great.

The Danganronpa and Ace Attorney games have some really good detective stories in it - I think the overall story in those 2 series is pretty bad, but in each game, there is at least one individual case that is great; and Zero Escape is one of the only work of fiction where I thought time travel / parallel universes was done right, without loopholes I could think of.