VNs, that made their mark on history, huh?
Well, first one that comes to mind is Katawa Shoujo, for giving everyone an easy introduction to the world of VNs.
Next would probably be Tsukihime, for it's revolutionary storytelling in the early 2000's.
Then lastly, probably Grisaia no Kajitsu for taking the much needed leap ahead for the localized VNs.