I dunno about favorite, but one manga that holds a special place in my heart is Yagyuu Hishou: Kaze no Shou (published in English as Samurai Legend and in French as Le livre du vent), written by Kan Furuyama and drawn by Jiro Taniguchi. It's about Yagyu Jubei foiling a plot by the former emperor Go-Mizunoo (referred to as "Go-Minoo" in the manga) to overthrow the Tokugawa shogunate, and his duels with a mysterious young ninja named Yashamaro. It's framed by the tale being told by Katsu Kaishu, a Japanese politician who in 1868 negotiated the peaceful surrender of Edo Castle to the Imperial forces led by Saigo Takamori, who would later go on to lead the disastrous Seinan War in 1877 (which is the loose basis of the Tom Cruise film The Last Samurai). It's a thrilling tale from beginning to end, and is full of surprises (such as the appearance of a young Matsuo Basho).