Sakabato(Reverse-Blade Sword):  Kenshin's main line weapon, mostly used for the series.  This weapon actually looks like a regular katana, however the blade that is used for cutting is on the wrong side.  So if you think about it, you could use your full power and not kill anyone.  Kenshin is pretty amazing with this sword, and is of sentimental value to Kenshin.  It's his symbol for repentance and shows he's no longer a murderer.

Katana(Japanese Sword):  The oldest, and most powerful killing utility for samurais.  The most often used sword in the series as well.  To me, it's the most traditional and well-balanced weapon in all of history.

Zanbatou:  Sanosuke's one-time-only weapon.  This is an ancient sword, and was barely used after a while because of its weight.  In the series, Sanosuke used it against his first fight with Kenshin.  Kenshin was easily able to destroy it.  After seeing its weakness, I guess Sanosuke got rid of it, seeing that it was too slow for Kenshin's god-like speed.

Wooden Sword:  It's basically a sword made of wood.  It's mainly used in teaching the Kamiya-Kasshin Ryu, the style that says that a sword should give and not take life.  It's not a very appealing sword to most people, but hey it's a sword.

Kodachi(Double Kodachi):  A sword that is half a sword.  It's a really good defense weapon, but the offensiveness of it isn't really that good.  Aoshi Shinomori first used one, but after Kenshin found a weakness in his offense, he figured 2 would stand a better chance against Kenshin, seeing that there will always be a free arm. 

Mugenjin:  The deadly sword that Makoto Shishio uses.  Basically a sword that can ignite flames while the user slashes.  But to get it to actually create fire, Shishio had to kill many people, and stab the sword inside human fat oil.  Enough of that will make it into a mugenjin like Shishio's