There is a lot of VN, but for me Hiiro no Kakera, Black Wolves are on the top of the list. And the games come very close of the VN so much I would recommend it to all to play and see
I've got a fair few favourite VNs, but one that I've really come to like recently after just finishing it is Steins;Gate and Steins;gate 0. Really got me hooked on time travel theory and had me doing research on some of the topics that came up in-game, like Kerr Black Holes.