So I've mentioned quite a few ninja movies. I know there are also a lot of manga about ninja, in fact the inspiration for a lot of these movies comes from manga, but I'm not a manga reader, nor a big anime fan, so I tend to watch more of the live action stuff. These movies can be used as good fodder for ninjas in an RPG.
Of course, there are lots of old Sho Kosugi (Enter the Ninja, The Master, etc.) and Sonny Chiba (all kinds of stuff) flicks to watch.
For animation, Ninja Scroll is a fun one. It follows the fantasy ninja idea that every ninja has some unique super power, but it's a good story and has some cool imagery as well.
For live action, one of my favorites is the remake of Owl's Castle. I've never had a chance to see the original, but I hear it's even better. The remake, staring Nakai Kiichi, tells the story of a group of Iga ninja trying to get revenge on Toyotomi Hideyoshi, heir to Oda Nobunaga (who destroyed Iga). Lots of fun, and it doesn't go overboard with the ninja powers. Just enough to make them mystical, but not super heroes in black pajamas.
Red Shadow: Akakage is based on an old Japanese kids' TV show. Sort of like the Lone Ranger, only with ninja instead of cowboys. Never saw the old TV show, but this movie was a fun one. It's a bit more of a popcorn movie than Owl's Castle, and the ninja are a bit more specialized (although not quite super powered like in Ninja Scroll).
Based on a manga, Azumi is techincally not a ninja movie--the characters are just out and out assassins, but they get trained in a ninja-style remote mountain village, and sneak around trying to kill Tokugawa Ieyasu's political enemies. It's a bit more action oriented, but it stars the sexy Ueto Aya, so why not throw it on the list? (Plenty of eye candy actors for the ladies in this one, too, if you like bishonen). Never saw the sequel, so I can't comment on it.
And the movie that we saw about half of over the weekend that prompted this whole Ninja Week idea for me was another one based on a manga called Basilisk. The movie is called Shinobi: Heart Under Blade, and it's a live action ninja-as-super-heroes type movie, but the first half had some cool fight scenes and special powers. The plot is basically Romeo is a Koga ninja, Juliet is an Iga kunoichi. Hijinks ensue. Again, only saw the first half, but that first half was interesting.
Please don't ask me about Ninja Assassin. 비 (Rain, as he's known in English) is a terrible pop singer, and an effeminate little twerp, and I just can't see myself paying money to watch him try to be a ninja. It does have good old Sho Kosugi in it though... Maybe I'll download it someday. Maybe not.