My favorite in this category has always been "Blood Magic"--it's posted on Schnoogle. There are, as you probably could have expected, many "Snape is Harry's real father" fics--there was a prompt a number of years ago (at least 8 years ago, holy cow) and a number of people jumped on it. "Blood Magic" was the first fanfic of any type I ever read though, and the fact that it was excellent is probably why I kept reading, so I will always be grateful :)
http://www.fictionalley.org/authors/gatewaygirl/BM.html