I have not read that many VNs, admittedly, but what few I have I did love! The exhaustive list:

Mice Tea: nsfw novel but deals with queer discussion and is so heccin amazing with it~!

Narcissu 1st: Very sad one following a girl's experience in a long term medical ward. Fair warning it deals with depression and suicide so it was a tough read at times.

To Whom the Bouquet Falls: An introductory modern fantasy chapter written by a very dear old friend of mine for NaNoRenO dev jam last year. Probly biased but I felt she did a very good job with it, even if it was just an intro chapter.