Samurai in Ninja Town

A specific trope focused on the popular concept that if Samurai are present within a given story, chances are that ninjas will follow, or vice-versa.

The idea bases itself on the premise of the samurai and ninja of Japan holding to opposing ideals, and yet both being considered Badass by the general public for their seemingly superhuman feats, skills and philosophies, even to the point of being historically inaccurate, especially in anime/manga.

Usually, one or the other is the protagonist while the other is the antagonist (usually though, the latter can be an army of Mooks.)

When the samurai is the protagonist, more often than not is (s)he a master swordsman who is either humble, or the silent type, able to slice a speeding bullet in two without even so much giving a snarl, as (s)he cuts armies of ninja down with a single swipe. As a mook? Usually the samurai is just a loud, bullying dumbass with a sword...live and learn.

In contrast, the ninja protagonist is clever and capable of numerous death traps and tactics, even using occult wizardry sometimes to literally burn through the opposition. As a mook? Slithery shadow thugs who're good at killing, but terrible when facing the samurai one-on-one.

Rare, but not impossible however, is the concept of both samurai and ninja protagonists working double-team, helping each other balance out weaknesses, but usually arguing about principles and combat stratagem. Regardless, when combined, armies tend to fall faster than sakura petals in a stiff breeze.

Examples of Samurai in Ninja Town include:

Anime and Manga

The Lupin III episodes and movies that focus on Goemon, such as The Fuma Conspiracy and Dragon of Doom, often have ninjas as enemies.
In Nabari no Ou, most of the main characters are ninja, but Raimei and Raiko identify themselves as samurai.
The Land of Iron, unlike the other lands in Naruto, has samurai (who look like Stormtroopers) instead of Ninja. This makes the Land of Iron a useful neutral ground for the leaders of the ninja villages to hold a summit. The samurai are fairly competent, using Chakra to create energy blades and seems to posses the same superhuman feats as the Ninja (minus Elemental abilities) but the regular samurai suffer from wearing face-concealing masks and lacking names as can be seen by the few Sasuke encountered and killed. Their leader Mifune, however, is able to hold his own against Hanzo, who was one of the most powerful ninja in the world. Mifune's specialty is using iaijutsu to disrupt ninja hand seals (required for the majority of their superhuman techniques), and is so fast on the draw that Hanzo concedes that attempting those techniques against him would be pointless.
The OAV Ninja Scroll has a Ronin named Kibegami Jubei fighting against multiple ninjas, from masters whose magical skills have turned them into monsters to Faceless Mooks.
In Samurai Champloo one of the main characters is a Ronin, a masterless samurai. Several ninja-like characters make appearances during the show and generally give the characters a fair run for their money, but the only person outright stated to be one is the baseball-loving, sunglass-wearing ninja in episode 21, who ends up shanghaing the main characters to play a game of baseball against a US invasion of Japan. In the 17th century.
In Samurai 7, a group of ninjas live under the city that the main characters visit, and threaten to destroy said city if not appeased with bribes.

Live-Action TV

The Sixth Ranger in Power Rangers Ninja Storm is the Green Samurai Ranger (his Sentai predecessor was a ninja like the rest of the team).
- The extra hero Ninjaman in Ninja Sentai Kakuranger had the ability to to transform into 'Samuraiman'.

Video Games

Muramasa: The Demon Blade has both ninja and samurai as enemies and allies at various points. The protagonists are a ninja and a princess who's possessed by the spirit of a samurai.
Musashi: Samurai Legend has Musashi, the heroic samurai, against endless Mooks of Ninjaroids, which is Exactly What It Says on the Tin; Ninja Androids.
Many samurai in Sengoku Basara have ninjas who serve them, so both types of character turn up as playable characters and enemies.
Tenchu puts players in the shoes of a ninja with plenty of samurai Mooks to assassinate.

Real Life

This trope takes inspiration from Real Life (and not just Japanese history) as it makes sense for warrior leaders (samurai) to send assassins (ninja) against their rivals before or in lieu of facing them on the battlefield.