As follows, probably my favorites are
DracoxHarry - Not the first I ever read (which was called Eclipse, by Mijan) but the best I ever read was Drop Dead Gorgeous (which is, sadly, no longer available.) It was how Harry had a very tiny strain of Veela blood via Lily and he and Draco are Auror partners...Much hilarity ensues. (I have a full copy, just pm me if anybody wants to read it.) (Also: A highly addictive song. -->
Listen!DracoxLuna - Dangerverse, by whydoyouneedtoknow. Amazing. Draco doesn't grow up evil Lucius Malfoy Junior, instead grows up, essentially as Remus's son, and meets Luna.
RemusxSirius - I think it all started when I read my co-author's story, Not Interested, about how Tonks fancied Remus and he didn't like it so Sirius took it upon himself to make the whole Order think that he and Remus were lovers.
Tom RiddlexHermione. Hermione and co go back in time to kill Voldemort before he becomes Voldemort. She finds out that Tom Riddle is very different from Voldemort. Completely AU. Oh...Uh, I should probably give the name: Have You Ever by Lady Moonglow (P.S: There's a trailer! -->
HEREAnd..from there it just disintegrates into various pairings.