Hattori Hanzo

A 17th-century portrait of Hattori Hanzō

If Sarutobi Sasuke is the Miyamoto Musashi of Ninjas, then Hattori Hanzō was definitely the Yagyu Jubei of Ninjas.

Put it simply, Hanzo was the Ur Example of Ninja, although his actual profession was 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.

Compare with Sarutobi Sasuke, Yagyu Jubei, also Oda Nobunaga.

Works in which Hattori Hanzo appears:

Anime and Manga

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.
In Naruto, Hanzo was the leader of the Rain Village and is a hyper-paranoid bastard, orchestrating Pain's Start of Darkness, and subsequently getting himself killed by Pain.
Hanzo's descendents are clanhead figures in Basilisk. His badassness is informed, as he's mired in politicking through the series, but his son can more than keep pace with the dueling ninjas enough to bring back reports without a scratch.
Also in Hunter X Hunter there's a ninja named Hanzo who was looking for the Hunter license to find a scroll.
Genderswapped into a Ninja Maid in Hyakka Ryouran Samurai Girls
Hattori Junko from Ichiban Ushiro no Dai Maou comes from a ninja family.
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 A Certain Magical Index is heavily implied to come from a prestigious Ninja family by Kuruwa (a female Ninja)
Hanzo serves as Ieyasu's right-hand man aside of Oukatsu in Brave 10. Definitely antagonist.

Film

Kill Bill: "Is that a Hattori Hanzo sword?" He lives in Okinawa and makes badass katanas. Remember: You Don't Sell A Hattori Hanzo Sword.

Live-Action TV

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 as a cover.
At the end of the 2010 Christmas episode of Leverage, Eliot gets a Hanzo Sword as a present from Nate and Sophie.

Video Games

Hattori Hanzo is a character in Samurai Shodown, as a Badass Grandpa ninja. Said game also features Yagyu Jubei as his friend.
And previously, there's also Hattori Hanzo from World Heroes as a young ninja with Anime Hair who just wants to be the best fighter ever.
Hattori Hanzo is also a character in Samurai Warriors, loyal to the Tokugawa, obsessed to the words "Shadow" and "Darkness". He's also acquirable as a bodyguard to spot hidden enemies.
Hanzo appears as an elite officer for the Tokugawa in Sengoku Basara 3.
In Suikoden, the leader of the Rokakku village (where Kasumi resides) is named "Hanzo".
Kenji/Mukuro from Red Earth/Warzard is based on Hanzo.
In Mortal Kombat, Scorpion's real name is Hanzo Hasashi.
- 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 who's 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.

Western Animation

In the ThunderCats (2011) episode "The Duelist and the Drifter," a legendary swordmaker makes his self-appelled Sword of Hattanzo, later sought after by the best swordsman in the land.