Kenshin-gumi: I believe Kaoru and Yahiko came up with the name. The Kenshin-gumi is basicly the main 5 characters; Kenshin, Sanosuke, Kaoru, Megumi, and Yahiko.

Juppongatana: Or the "Ten Swords" are Shishio's group that joined to be with him or against him, sorta like "keep your friends close, and your enemies closer".

Oniwabanshu: are the remaining group of ninjas that are headed by Aoshi. At the time of the Meiji Era most of the Oniwabashu left to start their own lives. A few stayed because they had nothing to do with their lifes but fight.

Junchuu Arc: or the 6 Comrades are a groupd of people that were gathered by Enishi. They each shared one thing in common, they all hated Battousai just the same and planned to avenge him.

OVA: Is the story of Hitokiri, Tomoe, and the reason of Enishi's hatered for Hitokiri. It tells the story of Kenshin's scar and the role he played in bringing fouth the Meiji era.

Movie/Filler Arc: This isn't an original Watsuki-sensei work but was created by the Kenshin story board group.

Other: Other characters that just don't really have a place in my other catagories, but they are just as important as anyone to the story! ^_^

I am big on originality and I focus more on the manga itself when I do these character bios. Because the anime sometimes does not run true to the original story, I decided to have my focus on the manga completely, unless specified so (In example, there is the movie and the filler section which is, of course, not part of the manga.). However, there are tuns and tuns of characters in Rurouni Kenshin and it is hard to keep up with all of them. This is why I decided to introduce a system that I call "Color Order." Each colored square represents where the character can be viewed. Some characters will have more squared than others, like Kenshin for instance, who is the hero of the sotry, has all the squares.
I hope this helps in your quest to piece together this anime.

manga
TV series
OVA
Movie
Jinchuu Arc
Filler Arc