Most of the female protagonist games use protagonist name like "Lisa drinks the water and dies" even if you're the one making the choices. Are there any good ones doing it like "You drink the water and die"?
I believe Corrupting Kayleigh uses the second-person pronoun; but it has been awhile since I played through it. May be worth checking out, I really enjoyed the game.
Haven's Port and Revamped Bloodline have this, I'm sure a few other HTML games do so as well. I don't remember any VNs that use the second person, but there probably are a few.