If you're looking for Aoshi-, Misao-, or Oniwaban-centric fic, Nagia's the author to check out. Her Aoshi is one of the best I've ever read, bar Vathara's, and her Misao manages to be both genki and emotionally mature. Of note are "These Cuts Of Mine" and "My Big Fake Ninja Wedding" (Better than it sounds, I promise).
Synopsis: A Rurouni Kenshin/Highlander crossover. It's a story about love, and loss, and moving on, with Kenshin as an Immortal. And you get one guess what Kenshin's opinion of The Game is!
Comments: The story doesn't require knowledge of Highlander, but it is set at a point where all the Rurouni Kenshin'' characters except Kenshin are long dead, so all the story's characters are dead or original characters. That said, the story gives an interesting look at Kenshin through a stranger's eyes and contains plenty of action without drawn-out descriptions of fights.
There is a prequel, A Life Lived (a not-quite-complete account of Kenshin as an Immortal) and two sequels, Walk Not Alone (Thirteen years of no contact later, Kenshin wanders in whilst looking for a damsel in distress.) and A Rurouni Goes to College(An 160-year-old Immortal goes to college. You'd think he was old enough to know better.)
Warnings: Violence level is about what you'd expect of Rurouni Kenshin. A couple of heterosexual relationships are seen, with the occurrence of smut implied.
The other stories in the series are equally or less violent, but some contain non-graphic abusive/non-consensual relationships and pedophilia. There is also some frank sexual discussion and a homosexual couple among the cast, in case anyone is bothered by those being considered acceptable.
Synopsis: "During a trip to Kyoto with his friends, Himura Kenshin winds up in deep water... thirteen years in the past. How will Kenshin deal with the Revolution again? And how will his friends deal with Battousai, who has traded places with him?"- author's blurb
Comments: A good read, with an interesting concept.
Synopsis: Katsura Kogorou, leader of the Choshu Clan, is captured and under a death sentence! Can Kenshin find and rescue him before he is executed? Set during the Bakumatsu, after Tomoe's death.
''One of the best fanfics I've ever read for Ruro Ken, it features Battousai Kenshin as he was in Canon as opposed to the Fanon interpretation. The action is great, the fights are well written and word can't really describe it, the story is incomplete and hasn't been updated in years but the last chapter ends at a point that can theoretically be taken as an ending. The lengths at which Kenshin will go to save Katsura is touching and awesome.
Synopsis: A red-haired, amber-eyed stranger washes up on shore in a small, seaside village.
''It's a great fic with well written O Cs that work really well with the story and no Mary-Sues whatsoever. It's an interesting concept/plot that I really wish would be used more often (or rather, used more often in a good way) and unfortunately the story is incomplete and will never be completed due to Hakubaikou's untimely death.
Synopsis: The story of the life, and love, which grew between an unlikely couple. Follows Saitou and Tokio from the Genji era through and past the Rurouni Kenshin tale.
Comments: As stated, this story follows the life of Saitou and Tokio, his wife in real life. Needless to say, things are somewhat more dramatic given that it's set in Rurouni Kenshin, but I don't want to spoil much. We do eventually get to see the Kenshin-gumi, but the cast of original characters are so well-developed that their presence is icing on the cake. Tokio is developed wonderfully, and Saitou's characterization is DEAD ON. You won't be disappointed.
Synopsis: In high school, Kaoru Kamiya escaped from a demon. Five years later, she meets a man who looks awfully familiar...
Comments: True, it's technically a High School AU, yet it's still one of the most engrossing fanfics I've read in a long time. It's so well-written that upon reading it again I could pick up new details I'd missed the first time. Half of one chapter is simply Kaoru, Misao and Megumi talking over lunch, and it's still not boring.
Synopsis: "She's got a scar where he cut her; she bled where he touched her; she left that town and never went back. But Misao can't stop thinking, "If I..." and she can't stop wondering if what he did stains her."
Comments: This one's a hard read, but ultimately worth it. She uses a light touch to drive her point in deep. Warning for rape aftermath.
Synopsis: "The early adventures of one Himura Kenji. He really causes his parents a lot of trouble, oro. But everyone loves him anyway! Fluff abound, as usual when concerning little Kenji. Leads in to Path of Swords." Kenshin and Kaoru pairing, of course, with a few moments here and there between them. Set when Kenji's 5-6, after the end of the manga.
Comments: I've checked out some of the other Gen Fics in this section, but it makes me a little sad that none of them revolve around Kenji... So here's one starring the little guy! It's not a pairing fic, though K&K get plenty of WAFF moments. It takes on some more serious matters toward the end, and leads into a very dark and serious fic called Path of Swords starring a fourteen year old Kenji.
Synopsis: When Kenshin brought Aoshi back to her, Misao thought he would never leave her again. But now Aoshi is on trial for his past sins, and Misao must decide, once and for all, what she is willing to do to keep him with her - because some things come with too high a price.
Comments: Come on, nobody really thought that the Japanese government would leave Aoshi alone without him even bothering to change his name, right? Angsty and yet delicious look at how the Meiji government would have reacted to Aoshi's return, with some interesting historical detail. (While it does focus on the connection between them, the nature of the relationship between Aoshi and Misao is left ambiguous, so I'm leaving it here.)
Synopsis: "Kenshin wakes with full knowledge of Kiyosato and Tomoe before he ever sees them. The future has changed. Welcome to the war." -from FF.net summary
Comments: Quite the "original story with a twist" type of fic here. Exciting and suspenseful from the beginning, with an interesting spin on the events we already know. The plot lines, characters, and background world are well thought-out and captivating; the author really draws you into Kenshin's mind and world. Fairly dark and violent, but not really worse than the original manga or OVAs.
Pairings: Mainly Sanosuke/Megumi with some Kenshin/Kaoru
Synopsis: "No longer a one-shot! Sano is a hooker, who gets picked up by the richest, and the coldest, customer of his career. But he doesn't turn her down, of course!" - FF.net Summary
Comments: A funny as hell twist of an AU Rurouni Kenshin fanfic. The premise is comedic gold, the characters are extremely well written and Aoshi is a pimp. Armed with a sword/pimp cane. Aside from Aoshi's pimp-ness, the story itself has a decent and interesting plot with fun little twists along the way. As this fic is rated M (and the premise gives it away) there is sex; but it doesn't take over the story, which is always good. I recommend it completely, for those able to deal with the mature content.
Synopsis: How the paranoid ninja leader of a paranoid ninja organization gets married: or, a practical lesson in Why We Do Not Listen To Okon.
Comments: A surprisingly believable Aoshi/Misao that grounds itself pretty thoroughly in what life running an inn would have been like for a bunch of paranoid ninjas. Also, why Aoshi can't get married like a normal person. Looks like it's going to be a delightful mix of "paranoid ninja shenanigans" and "rom com shenanigans."