If Sarutobi Sasuke is the Miyamoto Musashi of Ninjas, then Hattori Hanzo was definitely the Yagyu Jubei of Ninjas.
Put it simply, Hanzo was the Ur Example of a Ninja, although his actual profession was a Samurai and he prefered to ride into battle with a spear. Born Hattori Masanari, he was loyal to his lord Tokugawa Ieyasu. He made his debut in the battle of Anegawa, at the tender age of 16, and earned himself the nickname "Devil Hanzo". He was a master of Iga ninjutsu. His biggest accomplishment was during Ieyasu's perilous journey crossing the Iga village after fleeing from Akechi Mitsuhide's forces after Mitsuhide killed Oda Nobunaga. Using his ninja connections, Hanzo proceeded to secure a path for Ieyasu to arrive safely in his domain. His cause of death is unclear, some say he was lured into a naval battle against Fuuma Kotarou and got his ship burnt down. However, this is heavily myth-based; historical records would say he died of sickness.
While his name isn't used as often as Sasuke's in the world of fiction, Hanzo remains a popular figurehead of Ninja these days, despite his actual profession above. No one seemed to notice that 'ninja' was actually a side job for Hanzo.
In Samurai Deeper Kyo, Hanzo is featured, however, it turns out this "Hanzo" is the actual Tokugawa Ieyasu, who's also good with ninjutsu and guises himself as Hanzo, while having one fat lard to act like Ieyasu.
Hanzo's descendents are clanhead figures in Basilisk. The main Hanzo (Hanzo the first aka Masanari) badassness is informed, but he is the one who implements the whole Koga/Iga truce. His son/succesor Hanzo the Fourth aka Masahiro and his nephew and adoptive son Kyouhachirou also appear: Masanari does his best to monitor the Kogas and the Igas as the truce is broken and by the end he's one of the few survivors in this particularly cruel Kill 'em All series, while Kyouhachirou can more than keep pace with the dueling ninjas enough to bring back reports without a scratch and lives to tell as well.
Also in Hunter × Hunter there's a ninja named Hanzo who was looking for the Hunter license to find a scroll.
A ninja named Hattori Hanzo appears in the Oda Nobunaga Tournament arc in Yaiba as a secondary character. He looks like the traditional ninja and is one of the 8 strongest.
Another gender flip occurs in Sengoku Otome, where Hanzo is a Nerd Glasses-wearing ninja who assists Ieyasu from the shadows, though sometimes going overboard (i.e. burning down the stage).
Hanzo is just one of the many historical figures appearing in Billy Bat.
Hanzou from To Aru Majutsu no Index is heavily implied to come from a prestigious Ninja family by Kuruwa (a female Ninja)
Hanzo serves as Ieyasu'sright-hand man aside of Oukatsu in Brave 10. He disappears after Oukatsu perished, but it's later revealed that he had his own agenda of ruling Japan from the shadows, effectively making him the primary Big Bad, when Ieyasu is so far shown as ineffectual. He has his own band of dark ninjas, one of them, a Russian busty blonde ninja Anastasia, already sent to the Braves to spy on them, and mostly to drive his main target Isanami into despair so he could claim her power of darkness... which (un)fortunately kills him outright when he attempts to control.
Of special note about this Hanzo, though, is that he's one of very few named characters that is male, which is especially notable as every other named daimyo or daimyo underling in the series is either female or a villain with the exception of him, "Hideyoshi", and Saito Dosan. This actually makes the situation during the retreat when he and Zenki attack Yoshiharu more tense than it normally would be since up to that point...well, those three are a good half the male cast on their own in a Cast Herd of close to 2 dozen.
A Japanese TV series called Kage no Gundan, localized to Shadow Warriors, features several Hattori Hanzos, each descended from a previous one, and all played by Sonny Chiba. This is mostly important to Americans because Kill Bill features Chiba reprising his role as yet another Hanzo descendant: This one is a swordsmith that can make swords that can cut down Gods; he runs a sushi bar in Okinawa as a cover, but once The Bride finds and confronts him upon one of his disciples (Bill), he comes out of retirement and forges her a sword.
At the end of the 2010 Christmas episode of Leverage, Eliot gets a Hanzo Sword as a present from Nate and Sophie.
Interestingly enough, in the non-canon webseries Mortal Kombat Legacy, his (previously unnamed son) is known by the name Jubei.
Total War: Shogun 2 features clan Hattori (formerly a special edition bonus, now available as DLC) a great clan whose hat is Stealth- most of their units have 'Iga-ryu Ninjitsu,' allowing them to temporarily become hidden in the open, or harder to detect when otherwise hidden; they also have improved success chance for Ninja agent actions.
Saizo Hattori from Power Instinct is a subversion, since his first name comes from Saizou Kirigakure.
In Inindo: Way of the Ninja, he appears as one of the more powerful recruitable characters.
Hanzo appears as a warlord in Pokémon Conquest, serving under Nene of the ninja-themed Viperia kingdom. He specializes in ghost types, with Spiritomb as his starter and the Gengar line as his perfect link.
Hanzo's clan is a playable faction in Shogun Total War via DLC.