Man's Best Friend
Most armed characters in the manga use the katana, the Japanese longsword with a long curved blade originally developed for mounted combat and was first known as the tachi (which is used in this manga by Yukishiro Enishi). It was, however, eventually shortened into the katana we all know and love. The katana is a highly revered object and the act of forging it is an art filled with countless customs and traditions. Kenshin uses the sakabatou, a reversed-edged katana, with the blunt and sharp edges reversed. The traditional katana is often paired with the shorter wakizashi, which actually appears very rarely in both the anime and manga. Kenshin had a wakizashi when he was still with the Ishin Shishi but renounced it along with his katana. I don't suppose Arai made a reversed-edged wakizashi (and such a wakizashi would serve no purpose since it's not even big enough to clobber people with) so Kenshin remained wakizashi-less. Besides that, since battou-jutsu and iai-jutsu are meant to be fast-drawing techniques, there is very little room in them for the use of the wakizashi.
The kodachi, a short sword, appeared as a pair wielded by Shinomori Aoshi, who made good use of the shield-sword's attack and defense properties. It's also longer and more curvy than the wakizashi.
Another popular weapon in RuroKen is Sanosuke's ill-fated Zanbatou, which was originally designed for fighting cavalry (it is, literally, a "horse-killing sword") and can be used like a sword or like a spear. Sanosuke's Zanbatou, however, looks nothing like a real zanbatou. Kenshin couldn't have stood on a real zanbatou, and it's unlikely to bludgeon a person to death. A real zanbatou is a heck of a lot prettier than Sano's monster-sword.
Misao's kunai are also highly fictionalized versions of actual kunai. Kunai started out as gardening tools - like a trowel or mini-spade - and was not meant to be used as a throwing knife but as a stabbing weapon (it could be fixed as the point of a spear). It doesn't have much of a blade - only a sharpened tip.
All in all, all the weapons and fighting styles used in Rurouni Kenshin really did exist (except for the sakabatou, Kenshin's reversed-edge katana, which is entirely the author's brainchild), but their abilities have been slightly exaggerated. A katana, for example, could never cut through a cement block or the thick hull of an iron warship. The blade is astonishingly sharp, true, but it's not known for its endurance. Still, the martial arts aspect of the series is a big part of what makes it so enjoyable.