Yoshimitsu appears in both the Tekken series and Soul Calibur, though Word of God states they're two different characters. They are far away from the common depiction, however, acting more like Samurais on crack. Tekken's Yoshimitsu is a ninja thief who has become a full-time cyborg over time, while the one from the Soul series is the mysterious leader of a band of thieves, and the last survivor of an actual ninja clan.
Tekken also includes Raven, who's more a secret spy/agent with ninja stylings. He's, however, dowright appalled at Yoshimitsu's "un-ninja" quirkiness and is quick to try to correct him.
Kunimitsu and her daughter are kunoichis whose style of ninjutsu is highly kinetic and full of spectacle. Their techniques include fire breathing, imbuing their blades on fire, super speed, throwing teleporting kunais, etc. Theyre the ninjas who most represent the style of ninjutsu commonly seen in the media which is why they appeal to so many fans.
Soul Calibur also includes more "traditional" ninjas in the form of Taki and her student, Natsu. They come from a whole clan of ninja who defend Japan from evil spirits.
The Tenno (read: all the player characters) of Warframe, who are essentially space ninjas with guns.
In Shogun: Total War you can hire both ninja and shinobi as strategic units. The game makes a distinction between ninja (who assassinate enemy characters) and shinobi (who are spies, saboteurs and seditionists), although historicaly there is no such distinction. The ninja is also horribly outclassed at his job by the Legendary Geisha unit, an ultimate assassin which gets close to the target in her role as a geisha before killing them with concealed weapons, probably much closer to how real-life ninja worked. The expansion also allowed you to train small units of "battlefield ninja", tiny but elite squads which used stealth on the battlefield to get close to the enemy general.
The sequel has the Ninja and Shinobi as the same unit (it's called a ninja but refers to himself as both when clicked) taking over all aspects of spying, sabotage and assassination. The Geisha still exists but is also given a heavy nerf; while she can never be caught and killed during a failed mission, she's much more expensive, easier to spot than a ninja and just as vulnerable to enemy Metsuke. Also, the building that recruits geisha also allows for recruitment of rank 2 ninja, which when constructed in a ninja speciality province like Iga allows for rank 4 ninja straight off the bat, which horribly outclass the Geisha. Battlefield ninja, called Kisho Ninja, also exist, and are the speciality of the Hattori and Tokugawa clans.
Fall of the Samurai flips the whole thing around a bit further. It doesn't even have ninja agents, instead having the shinobi agent fulfill the same role as the ninja has in the base game. It really doesn't differ all that much from its core game counterpart, the core difference being that it has a slightly different skill tree and retainers. Oh, and the kisho ninja units are still around and recruitable by traditionally focused daimyos.
The Legend of Zelda has the Sheikah; an ancient, technologically advanced ninja clan dedicated to protecting the goddess Hylia and her descendents who would later became the Hylian royal family. They were skilled in both magic and hand-to-hand combat, while also using weapons such as kodachi, naginatas, kunai, and Deku Nut smoke bombs. Most of them were assumed to have died out during the Hylian Civil War (or even earlier) other than a few notable examples such as Impa and Sheik (who was Zelda in disguise) in The Legend of Zelda: Ocarina of Time, but by The Legend of Zelda: Breath of the Wild they finally make a comeback although they choose to live normal lives at this point.
The Legend of Zelda: Breath of the Wild has the Yiga Clan, who are a group of rogue Sheikah that dedicate themselves to killing Link and Zelda in order to allow Ganon to take over. They typically wear red and black costumes, but can jump an unsuspecting player by disguising themselves as civilians. The Yiga are somewhat of a reconstruction of traditional ninja, as while they wear noticeable clothing, they don't merely stand around conspicuously; they either appear suddenly in ambush, or disguise themselves effectively to look like ordinary people (although a savvy player can learn to recognize a disguised Yiga from a distance).
Radiant Arc: Tamotsu is a ninja who focuses on having high speed and evasion stats, along with skills to inflict ailments on enemies and buff evasion. He belongs to a village of ninjas that hides their location from all outsiders, including their allies in case they are ever compromised.
Squirrel Fish from Shiwuyu/Tale of Food despite being Chinese. He plays every part of the "shadow assassin" archetype straight except attire and coloring – quiet and reserved personality, Undying Loyalty and a combat style that utilizes knives, speed and stealth.
The Super Smash Bros. series has Sheik, who originally was a form of Princess Zelda in disguise but now is a separate fighter, and Greninja. Kat and Ana from WarioWare also appear as an Assist Trophy in Brawl and 4, where they use their katanas to attack as they dash across the screen at diagonal angles.
Elite Beat Agents provides an odd example. It starts as a subversion: Ken Ozu, lazy heir to a car company, is forced into a ninja outfit by his father and forced to retrieve stolen automobile plans from a rival company, despite having little to no talent. After this, however, the player's success (or lack of) determines what happens. If the player fares poorly, it remains a subversion, as Ken fails miserably whenever called upon to use his "ninja powers". If the player does well, however, it becomes a Double Subversion, as Ken runs smoothly through the "classic" ninja abilities and completes his mission.
Speaking of Andy, he's pretty visible himself in that bright white outfit and his long blonde hair. And doubles as a McNinja, since he's originally from Southtown.
Eiji Kisaragi is a more traditional example, hailing from a remote region of Japan and enters the King of Fighters to settle a grudge against the Kyokugenryu Team. Though he and his team end up being a comedic group of ineffectual"villains".
Spinoff Maximum Impact 2 introduced Nagase, another Highly Visible Ninja described in-game as "The Ninja Computer Geek".
Chiho Masuda is a rogue ninja, who wants to live a normal life, as a highschool girl. Which is why she fled her family to join the VG Tournament: in hopes of winning the prize money to fund her new life.
Her cousin, KyokoKirishima, is from one of the Masuda's branch families. She's been ordered to find and capture Chiho, or kill her if she refuses to comply. Kyoko succeeds in tracking her down and defeats her but she lets Chiho go, instead.
Samurai Shodown had a number of them, the most typical one being Hattori Hanzo.
Hanzo also appears as a ninja in the Samurai Warriors games. In the first game he was contrasted with Sanada Yukimura in a "ninja vs. samurai" way, but in the second game he's contrasted with Fuuma Kotaro, another ninja, in a similar way to their World Heroes counterparts. The other ninja is Kunoichi, an original character based on the Sanada Ten who supposedly did Yukimura's dirty work for him (subverting his own archetype).
Samurai Warriors 2 adds Fuuma Kotaro and Nene, although the latter is a samurai's wife whose "ninja-ness" is in being a gameplay replacement for the removed Kunoichi. (acknowledged by Hanzo, who, if they meet in one stage, would comment on her having gotten stranger, "since the last time we met.")
Hattori Hanzo was an actual legendary figure in Japanese history, rumored to have been a ninja as well as a pretty decent soldier.
Altaïr Ibn-La'Ahad from Assassin's Creed fits the MO of a historical ninja in that he is an assassin who escaped notice by blending in with a crowd, but lives in Crusader era Israel rather than feudal Japan. Ironically the historical Ḥashshāshīn, of which he is a member, acted far more like media depictions of ninja than actual Japanese ninja did.
Ezio Auditore in Assassin's Creed II is more or less the same, only he can swim, is Italian and FABULOUS!!
Ryu Hayabusa from the Ninja Gaiden and Dead or Alive franchises. The latter series has a few others, including Kasumi, Hayate, and their half-sister Ayane. Hayabusa in particular has the distinction of being known as the most famous videogame ninja in the eyes of many video game players.
A certain not very good Neverwinter Nights module had the player as part of a sect of female ninjas called Kunoichi (which happens to be a historically accurate term for female ninjas).
Ninja are commonplace in the Final Fantasy series, whether as a class to use, unique party members, or as random enemies. They often possess the Throw command (Which can turn undesired weapons into lethal projectiles), elemental ninjutsu, and the ability to dual wield weapons.
Final Fantasy XIV blends the pop culture portrayal of ninja with reality, as while they utilize the supernatural powers of ninjutsu, when it comes to espionage, the Doman ninja you interact with simply dress as commonfolk, generally donning their traditional garb only if they know they're going to end up in a combat situation. The sole one among their number who goes about perpetually in uniform is Yugiri Mistwalker, presumably because being an Au Ra (A race that only recently began immigrating to Eorzea), she's liable to draw attention to herself regardless of how she dresses.
Bakuryu becomes the chief resident ninja of the series from BR2 onwards and has the type of speed and versatility one would expect — from freely teleporting around the ring, to wall running.
Kohryu is a bonus character, who was introduced in BR3 and is essentially a Moveset Clone of Bakuryu. Though he lacks his ability to Wall Run, nor can he create body doubles. Kohryu was given unique abilities of his own, such as being able to temporarily immobilize his opponents with a stun beam, and fire his gauntlet as a multi-hitting projectile.
The village of Mizuho in Tales of Symphonia and its successor the village of Japoni from Tales of Phantasia are hidden ninja villages. Sheena, one of your party members, is from the former, and in the remake of Phantasia, you can get Suzu in your party from the latter.
The Shinobi series features hero Joe Musashi, who battles scores of enemy ninja in a variety of different situations, including while being on a ninja surfboard in the third game. Spin-off game Shadow Dancer starred Hayate as its heroic ninja, the PS2 reboot starred Hotsume, and second spin-off /Nightshade (Kunoichi) has the kunoichi Hibana.
In no particular order from Mortal Kombat: Sub-Zero, Scorpion, Reptile, Noob Saibot, Kitana, Mileena, Jade, Chameleon, Khameleon, Cyrax, Sektor, Smoke, Ermac, Rain and Frost. Fifteen ninjas in the course of one very ninja-happy series.
Technically, Sub-Zero's clan are the Chinese warriors that Japanese ninja ripped off, and they hate being called ninja. Not that it stops anyone...
Technically, only Scorpion is a ninja. Sub-Zero, Noob Saibot, Cyrax, Sektor, Smoke, and Frost all belong to the Lin Kuei. Jade is Kitana's bodyguard, who is a princess, and Mileena is a clone, both of whom would likely be trained in some form of self defense. Rain, also royalty, is also likely trained in self defense and Reptile is another bodyguard. Ermac might count just from the sheer amount of souls he is made with, probability might dictate one of them was a ninja in life. Most of them are made fairly moot anyways, as only Scorpion and the Lin Kuei are from Earthrealm.
Mega Man 2: Metal Man is also dressed like a stereotypical ninja, though instead of shuriken he hurls sawblades.
You can become a Ninja in Mega Man ZX and its sequel, by obtaining Model P or copying its data.
ZX Advent gives us Siarnaq, the one holding Model P (And that you later copies the data thus gaining his powers. His voice is robotic and monotone, kind of reflecting how a shinobi should control their emotions... That is, until you hear him laugh. Perhaps it has to do with him being betrayed by his friends and left for dead in his past?
City of Villains has Mastermind characters who summon ninja minions, and Stalkers who have the Ninja Blade (attack) and Ninjitsu (defense) power sets.
Sam Fisher in Splinter Cell is repeatedly confused for one by guards. Might go to the point of a running gag as whenever the topic is brought up in conversation the other guard calls them an idiot saying they don't exist. Possibly played for laughs as interrogating a certain guard will prompt him to ask you to kill him with your blowpipe. At one point in the first game, Lambert explicitly refers to Sam as a "SIGINT Ninja".
Guild Wars has ninja as well in the form of the Assassin profession. Their primary weapon consists of a pair of daggers, they can vanish in a puff of smoke and instantly reappear at at different spot, and they have a variety of spells that fit with the media portrayal of a ninja.
The Dark Templar of Starcraft are Alien Ninjas who can bend light to make themselves invisible.
Kisuke from Muramasa: The Demon Blade is an Iga clan ninja. This is notable because Iga was one of the actual places in feudal Japan where there actually were shinobi clan.
The Komoris in Red Steel are a clan of ninjas who fight with guns and poisoned swords, and yes, they wear the stereotypical black pyjamas. Scott himself gets to undertake some ninja training over the course of the game.
There are ninjas in Mad Karate Man that serve as obstacles to prevent your revenge against businessmen from being fulfilled. You can just click them away though.
The WarioWare games have Kat and Ana, twin ninja preschoolers!
A good number of ninjas feature in the Suikoden gameverse, most of them being more visible than not.
Mass Effect 3 brings us Cerberus Phantoms, which are ninjas armed with insanely sharp wakizashis and are protected by barriers. There's also Kai Leng, who's basically the boss version of a phantom.
In the Street Fighter series, Guy uses traditional ninjutsu with street fighting influences, Geki and Ibuki fits the popular image of a ninja, Zeku is a flashier ninja with some anime-inspired ninjutsu, and Balrog / Vega / "Claw" mixes savate, and ninjutsu, with bullfighting influences (hence his nickname of the "Spanish Ninja").
In Sengoku Rance, ninja units are among the various types available. While they generally have high Search stats (making them useful for strategic sabotage), they're also effective at tactical sabotage and assassinating enemy commanders in battle. They're not very effective toe-to-toe against warriors or foot soldiers, though.
Shinobi from Command & Conquer: Red Alert 3 are the Empire's infiltrator units, who can throw smoke bombs and shurikens, killing infantry with a single sword blow. While they can't use stealth (the smoke bombs only force enemies to de-target them for a few seconds), a single one infiltrating a tech structure will instakill all that player's T3 air units.
In the Sonic the Hedgehog series, Espio the Chameleon, ever since the Chaotix crew's return in Sonic Heroes. Complete with invisibility powers and giant shuriken.
Rogues of World of Warcraft can do things like turn invisible, flash step, walk on water, and pick locks. They also make use of intangibility, smoke bombs, poisons, and countless dirty tactics.
Pillars of Dust: Ichiro is a ninja-for-hire who has high strength and speed, low defense, and a Smoke skill that blinds enemies.
The Scyther, Nincada, and Shelmet lines all have ninja motifs. Curiously enough, they are all also Bug-type Pokemon (Scyther=praying mantis, Nincada=cicada, Shelmet=snail) as well.
Koga, the Poison-type Gym Leader from Pokémon Red and Blue, also has a ninja motif. He's training his daughter Janine in the art, and when he makes it to the Elite Four of the Indigo League in Pokémon Gold and Silver, she takes over the Gym.
Plus, in Hoenn and Sinnoh there are several kid ninja trainers running around.
"I am one of the Ninja Trio! Being discovered means I must battle!"
Furthermore, the moves "Double Team" and "Substitute" are based on popular ideas of ninja techniques.
Kalos introduces the franchise's strongest Pokemon example in the form of Greninja, the final evolution of the region's Water starter. It learns every single ninja-esque Pokemon move naturally (Smokescreen, Double Team, Substitute, and Spikes), along with having two new signature moves (Mat Block and Water Shuriken) that are also ninja-inspired.
You'll get a Ninja no matter what Branch you go on in Vanguard Bandits. What type of ninja they'll be is path-dependent though.
Aztec Wars has Ninjas, clad in blue, as one of the Chinese units (supposedly, the Chinese empire in the game has conquered most of Asia). They're the basic infantry unit, and they fight with martial arts.
Kaede in Duel Savior Destiny is a ninja and ridiculously formal, for which she gets mocked quite frequently. To Taiga's disappointment, ninjas from where she's from don't employ kunoichi, making her just a normal fighter instead of allowing him to have the sexy fun times he would like.
Cactus, the author of the game, seems to like ninjas. Ninja Flu features another one, this time wearing a missile launcher on his back, to destroy the falling bird flu-infected ninja angels (yeah, his games are weird sometimes). Saru Ga Daisuki features a ninja monkey as its protagonist, with a grappling hook-like tool and the ability to climb walls and ceiling, and a more regular, human ninja who can run and make really far jumps.
Shadow Warrior features ninjas as basic mooks; unlike most ninjas, they wear nothing but pants and shoes and tend to use firearms, though they toss shurikens as well sometimes. They also seem prone to committing suicide for no reason. Some of them are almost invisible.
Lo Wang himself is also a ninja, though he does not engage in much stealthy action in-game. The remake series, however, changes this, with the second game allowing Wang to go into stealth mode and deliver heavy damage with a single strike.
Bad Dudes features ninjas as enemies who kidnap the President of the United States, requiring you to step up and be a bad enough dude to rescue him.
The very obscure Return Of The Ninja is a Spiritual Successor of Tenchu in Game Boy Color, having you sneak through stages to avoid the next screen being filled with mobs and losing rank points for being detected. A Shout-Out it makes to Tenchu comes in the cards you receive after completing the stages or trading with a friend, where some cards makes visual reference to tools you use in Tenchu.
La-Mulana's Kosugi family are descended from ninja; Shawn, Lemeza, and Lumisa all use ninja infiltration techniques to investigate ancient ruins, and it's implied Shawn's father did as well. There are also more stereotypical ninja enemies that appear suddenly, attack, and vanish just as quickly.
Though they are not seen in-game, the player character in Tropico 4 can hire ninjas to infiltrate a heavily-guarded fortress in Tibet. Unfortunately, the price for genuine Japanese ninjas is too high to afford, so the player hires Chinese ninjas instead.
League of Legends features the Kinkou Order, ninjas dedicated serving the balance of power. They consist of Shen, Akali (a kunoichi) and Kennen (a yordle), and all of them are playable to varying degrees, Akali serves as a traditional assassination-based Ninja, Kennen is more about blasting your enemies with lightning, and Shen is an unusually tough ninja that is capable of tanking while having a body built more like a traditional ninja (not very big). They also get their Arch-Enemy, shadow-based ninja named Zed.
Senran Kagura is a series where sexy shinobi-in-training schoolgirls from different schools fight each others, and is some strange blend of comedy and drama : in spite of being heavy on the fanservice side (the series is marketed as cute & sexy hyper-breasted battle action), the characters are deadly serious about their shinobi duty, some of the backstories are quite dark and the worldview is rather truthful to the hard-boiled world one would expect from a ninja world.
Hiryu and all the other members of the Striders in Strider have all the visual style of ninja, but in truth their job occupation is better described as "mercenaries for hire". Officially, however, they are explicity described as having "descended" from the ninja of Japan.
Ninja Commando Ginzu from Captain Commando is a traditional ninja in a four-man band of misfits including a Mummy-like alien and a super-genius baby. He's also a master of the same style used by Guy.
Fire Emblem Fates has ninjas as a Hoshidan-exclusive unit class; they're fast and frail, use hidden weapons to attack, and can pick locks and open treasure chests, making them similar to Thieves from previous Fire Emblem games. The most prominent ones are Kaze, Saizo (Kaze's older brother), Kagero, and Asugi (Saizo's son/Kaze's nephew, with both Kagero and a Female Avatar among his prospect mothers); with the exception of Kaze (who follows the Player Character regardless of what path they choose), they will only join the party on the Birthright (and Revelation) path.
In Wii Play: Motion, the second level of Trigger Twist pits a shuriken-shooting player against a bunch of ninjas.
Ever-present in Klei's Mark of the Ninja. Often praised for being a particularly accurate depiction, as well.
Genji from Overwatch is a Cyber Ninja, though his gameplay is surprisingly close to accurate depiction of ninjas: really dependant on stealth (without having a skill that makes himself invisible in naked eyes, thus depending on finding a hiding spot and coming out in the right time) and eliminating stray targets and then swiftly getting out before being detected.
Hayato is a typical ninja, since his role (both in gameplay and in-universe) is stealth and infiltration. He's masked and his abilities include attacking a single target with a Ninjato (on the ground or by jumping from above), throwing a shuriken, or climbing on roofs with a grappling hook.
Aiko fits well the female archetype. She can wear disguises (especially a geisha costume) and distract enemies; she also can temporarily blind them with sneezing powder and stab them with her hairpin. Like Hayato, she also has a grappling hook.
Yuki is a borderline example. She's not supposed be a ninja in-universe (she's a kind of vagabond teenage girl living as a trapper and thief), but her abilities fits the trope too, since she can stab enemies with a small knife, set traps, use distraction (with a flute), and pick pockets. She also has a grappling hook.
Akane the Kunoichi features them (as the name obviously suggests). Besides Akane, most of the enemies she fights are also ninjas of some description. Some just try to charge her, but others can throw kunai like she does (albeit only one at a time and much slower).
The Legend of Kage has the titular Kage (pronounced "KAH-geh") rescuing a princess using shuriken and daggers used as swords.
The Last Ninja series for the Commodore 64 (with the second game later ported to the NES as just The Last Ninja) centers on a ninja attempting to settle the score with an evil shogun.
Sekiro: Shadows Die Twice has you play as the ninja bodyguard Wolf, who will need to rely on a combination of swordsmanship, stealth, agility, and the many gadgets contained within his prosthetic arm (ranging from a grappling hook to firecrackers) in order to aid his young lord. However, included among Wolf's many foes are a number of other highly skilled and agile shinobi with their own techniques, the two most notable being Wolf's former mentor Lady Butterfly with her illusion magic, and Wolf's foster father Owl, who has many of his son's tricks plus a few of his own.
ARMS has Ninjara, who is a college student from a university of ninjas. He enters the ARMS Competition as his own senior project. One of his ARMS; the Stun-attributed Chakram, which is a typical ninja weapon and is also a equipment for the ARMS fighters, mainly him. Ninjara's ability in battle includes disappearing which can be activated as his air dodge or more especially he can use this while blocking an opponent's punches.
Virtually everything about Ninjala revolves around this trope; fashion, culture, and especially the titular sport. An organization is built with the sole purpose of preserving ninja history and the sport and the scientifically enhanced bubblegum serves to unlock the potential of any kid with ninja blood. The same gum seems to have a Fountain of Youth effect on adults.
The plot of Ghost of Tsushima revolves around the samurai protagonist having to learn to fight like a ninja to repel a Mongol invasion. Many of the "ghost weapons" in the game resemble classical ninja tools, such as kunai, smoke bombs, and a blowgun with poison darts. The Ghost Armor set (which provides bonuses to stealth) resembles classical ninja garb. There is some downplaying since the actual words "ninja" or "shinobi" are never used - since the concept does not exist until the "Ghost" brings it all together.
The Taimanin series focuses on ninjas that fight demons in the near future (Taimanin in Japanese translates to "Anti Demon Ninja"). While most of the series is notoriously Hentai, Action Taimanin, the primary non-hentai game of the series, places huge focus on stylish Hack and Slash action, with many Taimanin employing some manner of supernatural abilities, such as Asagi's speed, Sakura's shadow powers and Yukikaze's lightning, which she uses her guns as a focus for.
The Shinobi from For Honor is explicitly a Ninja, a member of a secret order that was hidden in the Myre until the ongoing Forever War brought them back into the open. Appropriately, their Weapon of Choice is the Kusarigama, which can be used to pull enemies down for attack openings. According to the lore, the Shinobi taught some of their secrets to the Orochi, who are something of a Samurai Shinobi.
The Game ModRidgeside Village has the Cult of the Lady with the Red Tail, which members are ninjas that identify themselves by wearing a red scarf. They use katanas and kunais as weapons and vanish using Smoke Out techniques.