Magic: The Gathering: All "proper" ninja (not counting changelings et al.) so far come from the Betrayers of Kamigawa expansion set. They all have the ability (known, of course, as ninjutsu) to pop into play by replacing an attacking unblocked creature on their side plus a variety of followup abilities that trigger off of their dealing combat damage to a player. The implication of this is that an individual ninja can masquerade as absolutely anything, from a flock of squirrels up to an Eldrazi. Talk about Paranoia Fuel...
Yu-Gi-Oh! contains a whole lot of ninjas. A trio of them even serve as a Shout-Out to Konami's popular video game series Ganbare Goemon.
The Complete Adventurer expansion for 3.5e features the Ninja base class. They are a viable alternative to the traditional Rogue, trading in more efficient sneak attacks and extra skill points for supernatural dodging and, at higher levels, the ability to turn invisible or incorporeal for a short duration.
The 3.5 splatbook Tome of Battle gives us the Swordsage, a highly versatile class that can fulfill many roles in a party, their most common role being that of a secondary meleer. They have plenty of maneuvers to help with whatever concept you could try to make, and one of the easiest is that of being a ninja (Shadow Hand maneuvers, specifically; things like shadow teleportation and precise, crippling strikes are the meat of the discipline). There's even a prestige class for them, called the Shadow Sun Ninja.
Ninja have, in various forms, been present as a class throughout several editions. 1st Edition AD&D featured them as a complicated 'secret' class you had alongside your public class (on pain of execution if you were revealed), 2nd Edition retooled them as a more standard class, 3E/3.5 featured several ninja Prestige Classes as well as the aforementioned 3.5 base class, and 4E had ninja as the name for a suggested build for the assassin class. In 5E, monks who follow the Way of Shadow are explicitly described as ninja, though rogues are often treated as an unofficial alternative by players (and multi-classing the two is very popular).
Exalted: Each type of Exalt has at least one caste that focuses on stealth, deception, and similar acts of larceny. Sidereals fit the ninja archetype best, though, what with their being snapped up and subjected to intensive training within days of Exaltation, their undisputed mastery of martial arts, their residence in a hidden community that most in Creation can't even find, much less enter, and that whole business with the Arcane Fate that makes them all but impossible to track or keep records on (or even, for that matter, remember clearly). The term 'fate-ninja' really sums them up very nicely.
Feng Shui lists the Ninja as a PC archetype. Their Martial Arts skill and Fu attributes are just one point lower than the Martial Artist, and they have the second highest Intrusion skill in the game (the Thief has the highest with a 16 AV). In addition, one of the Fu paths of the game, the Path of the Shadow's Companion (renamed Path of the Ninja in Feng Shui 2), is tailor-made for the Ninja, with powers that allow you to make silent martial arts attacks and bypass the Toughness of your opponent when attacking someone unawares. You also get to fight ninjas a lot as both mooks and named characters.
Legend of the Five Rings: The Scorpion Clan, especially the Shosuro Assassins and Bayushi Ninja Infiltrators, plays the trope straight and subverts it at the same time: the real assassins rely on disguise to blend into the crowd, while the "typical" ninjas in black pajamas are Highly-Visible NinjaMooks often used as a distraction.
In fact, the ninja mooks are aspirants to be "proper" shinobi; if they can survive trying to be "stealthy" in the worst way possible for a year, then they're ready to learn how to do it right. The books even point out that "ninja" gear, by and large, is completely awful. Never use a ninja-to against a katana, for instance.
One of the books states that all Clans have their own ninja-style groups, like the Daidoji Harriers of the Crane Clan (who focus on guerrila tactics) or the Ikoma Spymasters of the Lion Clan (who focus on information gathering). This despite the fact that ninja are outlawed by Imperial Edict, and thus do not officially exist.
GURPS: The ninja from GURPS: Dungeon Fantasy is a mix between the thief, artificer and swashbuckler, even getting a whole installment of the series devoted to it.
Paranoia: In the adventure "Warriors of the Night Cycle", from the Acute Paranoia supplement, the High Programmer Hik-U-VRS creates a group of elite stealth warriors with the skills of the Old Reckoning ninja.
Pathfinder has ninja as an alternate class to the core rogue class. Mechanically it combines some features of rogues and monks, with more focus on poison usage, rapid mobility, and leaving no trace rather than the rogue's trap skills.
Shinobigami is a "Modern Ninja Battle RPG" involving different ninja clans working to advance their various agendas.
War Games
Warhammer 40,000: Adamus Assassins are sword-carrying assassins who wear all-black, face-covering uniforms, specialize in surgical decapitation strikes, and are said to have their origins in martial traditions from Old Earth's Pacific region.
The Skaven of Clan Eshin are essentially ratman ninjas. They learned the arts of stealth and subterfuge in the setting's Fantasy Counterpart Culture of Japan, Nippon, and make heavy use of ninja trappings and aesthetics such as Stock Ninja Weaponry, a well-earned reputation for espionage and assassinations, shuriken, and all-concealing black outfits.
The Assassins of the Dark Elves take several elements from this archetype. Their leader, Shadowblade, is so awesome he can disguise himself as a mook of the enemy army. Even if they are composed of magically-reanimated corpses. Did we mention his skill with weapons is so great he can match an incarnation of the God of Slaughter in terms of sheer skill, and outmatch it in speed?
Ogre Maneaters are a special units in the Ogre Kingdoms army, consisting of ogres who've served as mercenaries in the many armies of Warhammer. Thus you can have an Imperial ogre, a pirate ogre... and, you guessed it, a ninja ogre.
A fan-made army book for Nippon gives them squads of ninjas as a Special choice whose main strength is mobility, and individual elite ninjas as Hero choices that function like Dark Elf Assassins.
