Not websites I know, but AOL instant messenger is really good these days. Gnutella is actually pretty alright. There was a brief cultural moment a few months ago in Shoreditch when some hipsters started using myspace again, but that seems to have petered out. I've heard it claimed that MetaFilter went through a bad patch and then recovered - not involved enough to know anything more about that though.

Good question, and I'm curious to see if anyone can provide an example.