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In terms of influential/genre-defining works, the medium has many:
> Rance/Toushin Toshi
> Tsukihime
> Muv-Luv Trilogy
> Ever17
> YU-NO (haven't played, but I know its influence)
This is primarily me saying that these are the biggest "pure" visual novels in the medium.
The big 3 visual novels in my opinion are Fate/Stay Night, Clannad, and Steins;Gate.
These are 3 works that have very strong acclaim while also reaching some level of mainstream success within their respective genres.
They are must-plays if you're interested at all in the medium.