The Route to Advancement by magog_83 - this links to the fourth story, but the other three are linked at the top.
I love this story. Very few writers I've read can base an entire story around an OC and still make it so canon you really, seriously know you saw Percy in the eps. It's especially impressive because it's not only how Percy gets to know Arthur and Merlin and observes their adventures, but also brings a slightly different view of court and Camelot from the point of view of the average knight. I mean, this is fun. And Brutus the horse is awesome.
Ten Weeks by shinetheway/shinetheway, sequel to Truth Is a Whisper - I was like, ecstatic when shinetheway sent me bits of this to read (she was out of the country and I am a clingy friend who goes into withdrawal when friends are gone; luckily, she worked out the best way to limit my whining "WHY DID YOU LEAVE ME ALONE TO DIE ALONE HERE ALOOOOOOOONE" and send porn. Genius.)
Not just porn, but a wonderful post-Truth Arthur in the weeks after, with a new relationship, a new reputation, and the sudden, dizzying changes of falling in love, losing your virginity, and maybe fighting a duel. And still utterly drugged with sex. I had a great time reading it, both for the hotness and for how well Shine nailed Arthur's confusion and lust and affection and utter bemusement at how quickly everything can change.
Truth North by the_moonmoth, Merlin/Arthur, futurefic - the future is now. Or, Arthur's come back again and they go on a road trip. I love this. The perfect Merlin, the richness of shared history and shared memory, the wistful tone of helpless hope when Arthur's return is a harbringer of something going wrong in the world that his birth is forever designed to subvert, and the way that Merlin's lived this so many times and still wants it so badly and aches for the inevitable loss of this before it starts all over again.
This just broke me, in a good way. I like to think one day, they'll be allowed to rest together. But for now, they still have work to do.
Actually, this idea is one of the most addictive that I've read and the author blows me out of the water being so careful with tone it wasn't until afterward that I felt a chill, the implication Arthur's birth and life are literally a part of the cycle of the universe correcting humanity before they destroy himself.
I think this would make an interesting result of Nimueh and Merlin meddling with life, death, and fate to indenture Arthur to humanity's fate, returning when needed to be awesome and world-saving and then dying until he's needed again. I'd had hazy thoughts in that direction, but it really hit home when Merlin thinks about what Arthur's degree is in this time around.