I've only played a few VNs, but this one haunts my imagination even after only playing it once.
Without giving away too many spoilers, it also plays with the medium of VNs in far as how the story is told to a degree. I like it when VNs do this well and show how they are unique as a medium as opposed to simply a LN with pictures. Ever17: The Out of Infinity is probably the best at doing this that I've read, but Saya no Uta is close.