Decepticon was right. Found out that it represents the Tokugawa shogunate, and a variation is used for the Tottori region of Japan.
http://www.japan-guide.com/e/e3010.htmlAlso found out that Lesayu Tokugawa, for whom the crest and shogunate are named after, is in the video game Samura Warriors.
The only reason why I can think of that it's used in Kill Bill is because that era was the last real era for swords and samurai before the Meiji era began and eliminated both, and it may be a tribute to that.