A while back I read this fic in which no one knew Tony was Iron man, not even the avengers they just thought he was their sponsor. Steve thought Tony and Iron man were dating and because Tony was hurt a lot, from missions, Iron man was abusing him. I think I read it on ao3.
I've read a few fics where Loki becomes an avenger, but I'm wondering if there are any long, well written series out there. It doesn't even have to have him becoming an official member of the team, as long as he's a good guy, and is on good terms with the team (kind of like the Housemates series).