Late to the party but I've been reading Full Metal Daemon Muramasa over the last week. Finished fukushuu-hen and eiyuu-hen so far.
My god, this is one of the best stories that ever came out of Japan's entertainment industry. It tackles so many so very complex themes with such amazing writing and characters...the final parts of eiyuu-hen just blew me away. This is so far above any other VN I've ever read, it's not funny.
Also, dat OP-Theme:
http://www.youtube.com/watch?v=Le2zxWrD294