ATLANTIS:
I am starting this particular section off with the one story that totally sucked me into the fandom. For Atlantis, it was Transcendental, a totally awesome fic by Shalott. I could read this once a week and never get tired of it. Go find it here: http://www.intimations.org/fanfic/#atlantis
I have put a ton of Atlantis recs on my live journal which is at: http://ladyra.livejournal.com/