Checkmate'verse by beadattitude - Sheppard/McKay. Sheppard gets turned into a cat, right, but it's so much more than that. It's a collection of stories that just--to say this is my happiest place is to understate it. Your husband/wife/SO left, your dog/cat/pet died, your house/apartment/residence burned down--you go read this. It is that good. I did a longer rec of this one here and I stand by the fact that it's one of the few and far-between fic that just makes me melt in utter bliss.
Misrule by thehoyden, Merlin/Arthur - this is freaking hysterical. Saturnalia in Britain! Merlin the Maiden! Tournaments! Fun! Yes, all of this and more!
Treason to Us by janne_d, Merlin/Arthur - one of my favorite angsty Arthur finds out. I love the progression, I love how Arthur thinks about it, and I love how well the author shows both his betrayal and eventual understanding.
Building a Bridge by berusama, Merlin/Arthur - okay, this just works for me. Revengefic with porn. Awesome.
Details in the Fabric by minarchy, Merlin/Arthur - mob AU! That's--well, really all you need to know. Based on a Merlin comic linked in the story.
ETA: Part 2 of Details in the Fabric. I'm really interested in seeing where this goes.
To Be Known by esohpe, gen - gen by way of very slashy. Another fantastic Arthur finds out, visceral, brutal, and painful to read. Also very true to what I think the initial reaction might be.