Hm I don't know very many but here's the ones I liked.
1) Samurai Champloo | a personal fave of mine. <3
2) Drifters | it starts out in that time period at least
3) Rurouni Kenshin
4) Gintama
5) Sengoku Basara
I've also heard Hakuoki is really good but, I haven't seen it.
