Beam Me Up, Scotty!: For fans who read fan fiction, it's an accepted phenomenon that Kaoru's favorite scent is Jasmine (and to a lesser extent, Kenshin is often associated with sandalwood, or something), even though the only character in the ENTIRE series to have a scent associated with them was Tomoe and her plum blossoms.
Cowboy Bebop at His Computer: A frequent victim of this, even in media that focus on anime and manga. Kenshin is not and was never a samurai, as that was a distinct social class one had to be born into. One of the English dubs even gets it wrong with the title itself. A similar problem exists for attribution of the theme "Sobakasu", as "Judy and Mary" was the name of the band, not anybody in it. (The singer is Yuki Isoya, who goes by "YUKI" in all-caps).
Creator Backlash: Watsuki has expressed regret at creating Raijuta. He's often cited as saying that Raijuta is his least favorite character.
Yahiko, like Kenshin. In the dubs, it's case by case.
Soujirou in the original.
Curiously averted in the Colombian Spanish dub, as all the characters are voiced by people of their respective genders, including kids.
Executive Meddling: In his original conception, Kenshin was supposed to be ''at least'' 30. But Nobuhiro Watsuki was told that "30 was too old for a primary protagonist in Shonen Jump." So, Watsuki dropped Kenshin's age to 28. (Thus keeping the concept of a more seasoned protagonist than the typical of the Shounen genre, but also making Kenshin young enough to be "acceptable".) Lampshaded in series, when Kaoru tells Kenshin he "can't possibly be 28", and Kenshin asks "Would 30 make you happier?" and Kaoru replies that it would not.
Hey, It's That Guy!: The live-action film involved Kamen Rider Den-O as Kenshin. Bonus in that Takeru Satoh, the lead, recently portrayed another historical assassin, Okada Izo, in the historical drama Ryomaden (which was apparently why he was chosen in the first place). The director of the film, Keishi Ootomo, was himself the director of Ryomaden (and, as you will see in the list below, the Ryomaden-affiliated cast is pretty much his Production Posse for this film series).
Ryunosuke Kamiki, known for voiceovers in Spirited Away, Howl's Moving Castle and Summer Wars, as well as Minamoto no Yoshitsune (both as a child and as an adult in Yoshitsune and Taira no Kiyomori, respectively) shall be Soujirou.
Yukiyoshi Ozawa (Kiso/Minamoto no Yoshinaka from NHK's Yoshitsune and Saigo Takamori from Atsuhime) shall be Ito Hirobumi, the first Japanese prime minister.
Hilarious in Hindsight: Watsuki-san noted in his character profiles that he based Kurogasa/Udo Jin-e on the historical assassin Okada Izo. Fast forward today where (as detailed above) Takeru Satoh, who played Izo in Ryomaden, plays Kenshin. This comes full circle when the film incarnation of Jin-e, who was based originally on Izo, claims to be a more genuine assassin than Kenshin-as-Battousai. Trippy? You bet.
Back in Kamen Rider Den-O, Takeru Satoh played Ryotaro, who is the nominal Kamen Rider, a living anomaly referred to as a Singularity Point. How does one mark a point? With an X.
He was known for saying "henshin", now he goes by Kenshin. Not hilarious but definitely silly.
Lying Creator: Watsuki has admitted (in the sidebars titled "Watsuki is a Liar"), among other things, that "rurouni" is a word he made up.
Role Ending Misdemeanor: Or at least a variant of it, involving associated musicians. L Arc En Ciel's "Fourth Avenue Cafe" was used as the fourth ending song for four episodes, but when the band's former drummer got busted for drugs, the resulting controversy caused the producers to pull the song and switch back to the third ending for another seven episodes.
The author originally intended for Usui to be a Terminator-style manhunter, pursuing Kenshin relentlessly through darkened city streets. Instead, we got theabove.
Henya was originally going to be introduced as a villainous character during the Kanryu arc; also, he was originally going to be in an aerial battle with Kenshin, but Watsuki changed this because he felt Kenshin would have been too strong an opponent.
According to Watsuki, Raijuta was originally supposed to be as imposing as he looked, but Villain Decay gradually set in.
Senkaku (Shishio's henchman and villain of the Shingetsu village mini arc) originally was going to be a member of the Juppongatana, and a speechless, beast-like brute.
The manga was originally going to be much shorter than it turned out to be, revolving around the Jinchuu arc.
It was originally going to be revealed that Hannya had been stepped on in the womb like the The Elephant Man, explaining his featureless death-mask of a face. Watsuki realized the Unfortunate Implications of that idea, and altered the backstory to Hannya having intentionally mutilated his face so that he could easily disguise himself as just about anything.
There was a pilot chapter in which Megumi (a rather weak-willed woman barely holding the family together), Kaoru (a tomboy Tsundere serving as the acting dojo-master), and Yahiko (a brat of a kid who feels like he has to be the man of the family since his father died) are siblings.
There's also a proto-story of Kenshin meeting Damsel in Distress Chizuru, who gifts him a ribbon to tie his hair back up when he loses his original ponytail tie in a fight. Chizuru lives on in cameo form at the end of the controversial second OVA, as the girlfriend of Kenshin and Kaoru's son Kenji.
Watsuki mentioned in his notes his concept for a fourth arc of the story which would revolve around Kenji competing against Yahiko and Tsubame's son to inherit the reverse blade. Interestingly, Kenji Himura would most likely been the antagonist of the arc, from what Watsuki had stated about his concept. That, plus the fact that the story would have been set in the beginning of Japan's move towards nationalism and militarization makes one wonder what the story would have looked like...
Originally, Fuji was going to actually take on Okina in battle. However, the author thought that a battle of old codgers wouldn't have been interesting.
Word of God: Watsuki himself has said that the series ended the way it did specifically because it was a shonen series.