A powerup in the NES Ninja Gaiden allows Ryu to create up to two red doubles that follow his movements. They can also hang in the air and attack if you move right.
The Freedom Force villain Déjà Vu, who spoke in rhyme and could clone himself indefinitely until the original was knocked out (said original being easily detectable since he's the only one with a full life bar). The sequel, Freedom Force Vs The Third Reich featured the WWII era Japanese villain Red Sun who had a slight variation of this power: he couldn't clone himself indefinitely but the clones became stronger and regained health whenever one fell in battle, hence they had to be dealt with one at a time. This variation in powers was most likely a reaction to the fact that some players would grind Déjà Vu's clones for infinite prestige points.
In Dota 2, there is a hero called Phantom Lancer who can passively create clones on attacks. And he can throw spirit lances that create clones. And he can teleport... creating two clones for distraction. Don't forget the purchasable item and rune that clones its owner.
Also there is a hero called Meepo who's ultimate skill is a passive called "Divided we Stand." Every time you take a level in this skill a copy of meepo will appear. Unlike Phantom Lancer who's copies are all expendable and far weaker than the original, each Meepo clone (up to five Meepos total) is almost as powerful as the original, sharing most of his stats as well as whatever boots Meepo is wearing. Each Meepo can be controlled individually to collect experience and gold across the map, as well as serving as a teleporter pad for other Meepos to arrive at. The tradeoff for this is that if a single Meepo is slain, every Meepo on the map instantly drops dead and you get put out of the action for a while. Meepo is generally considered a lethal joke character and is rarely played due to his high difficulty.
In Heroes of Newerth, there's a special power up that clones you twice. You can also clone yourself by using an item, the Geometer's Bane, and some heroes can do it on their own.
In Super Mario World, some Chargin' Chucks can split into three identical copies, which all then proceed to attack.
Several attacks from the Mario & Luigi series have 3-4 Marios and Luigis on the screen at once. Taken Up to Eleven in Mario & Luigi: Dream Team; while the Mario Bros. are in the Dream World, Luigi can multiply himself scores of times over, whether in order to explore areas (e.g. with a pillar of Luigis) or to fight enemies (e.g. with a big rolling ball of Luigis).
The Double Cherries of Super Mario 3D World make a copy of the player character for each one grabbed. Including Bowser.
In the tactical RPG Kartia: The Word of Fate for the PS1, the elf twins have this power, though it's only visibly used by the male one near the end of the game in Toxa's scenario.
Etrian Odyssey III: The Drowned City has a Ninja class; one of their moves lets them create a shadow clone to fill the usually-vacant sixth slot in the usual five-man party. However, they can use this to fill any empty slot... potentially resulting in a small army of fake!ninjas covering for the real one.
MARDEK Chapter 2, in which your first mission includes killing a guy who is "actually five blokes in one" or something like that. Magic theives.
Agent 47 of Hitman is a clone of himself, being 47th one. He ends up fighting a lot himselves and in some cases his clones are trying to assassinate him. Er, it's complicated. Anyhow, he's apparently the superior clone.
One of the three human civilizations in the Endless Space is the Horatio, after a beauty obsessed trillionaire discovered a Precursor cloning machine, and used it to build a massive Egopolis. Naturally, one of his faction traits is having higher population cap than normal...
In Kingdom Hearts, this is the ultimate plan of Xehanort, with the reason he created Organization XIII being so he could commit Grand Theft Me on the other twelve members.
Kingdom Rush gives us the Demon Legion, who can create an exact copy of itself with the same health as the original. Better put the hurt on them before they do so!
In Borderlands: The Pre-Sequel!, the playable body-double of Jack can create holographic decoys to attack enemies, as well as to draw enemy fire. Depending on how they're upgraded, they can function as Action Bombs, have a chance to be upgraded to Badass-tier or even count as a kill for the original so that he's revived when downed.
In Phantasy Star Universe, one of the NPC's Ethan encounters is a CAST named Lou. Later in the main story, Ethan works with Lou again, but she doesn't recognize him. It turns out Lou is a mass-produced CAST built and deployed by the government, and there are hundreds of her out there. Though you run into "Lou" a number of times in the game and its expansions, they are never the same individual. One mission even has you helping Lou rescue another Lou.
Tales of Maj'Eyal's 1.3 reworking of Temporal Wardens gave them a few abilities that involve calling on other timelines' versions of oneself for temporary aid.
Shin Megami Tensei IV: Apocalypse builds on the idea of Hordes from IV by making the third-to-last boss a Horde of Metatrons. Furthermore, the first form is the Final Boss is comprised of an army of YHVH heads, with a few in particular getting in attacks.
Virtue's Last Reward has this as the villain's ultimate endgame... well, sorta. Dio is a Myrmidon, a clone of Left, the murdered brother of... Brother, the head of Free The Soul who believe that the human subconscious has been poisoned by negative emotions. To heal humanity's collective mind, Brother tried to exterminate humanity with Radical-6 (And nearly succeeded) and is now trying to replace humanity with Myrmidons who Brother believes to be pure beings.
BloodRayne featured Hedrox the Infinite, a bestial vampire that had the power to duplicate himself whenever he is dismembered. Coupled with his extremely fast regenerative powers and new Hedrox clones being created out of his severed limbs, its nearly impossible to defeat him... Unless if him and his clones are dropped on water, which is like acid to him.
The two Styx games Styx: Master of Shadows and Styx: Shards of Darkness make use of this. Goblin protagonist Styx can vomit out clones of himself which serve a multitude of purposes. If you are chased, they get killed instead of you. You can control them and let them explode as smoke bombs to get cover. In the second game you can make the smoke poisonous and later let clones explode to kill everything in a 2 meter radius. Also in the second game you can assume the control of a clone when you die, provided you have spawned one beforehand. It is also important to the plot, as the player character of the first game is just a backup clone of Styx, which you find out halfway through the game. At the end of the first game you fall into the magic soup you use to create clones and unleash the goblin plague that is a plot point of the second game on the world.
During the Cross Ange finale in Super Robot Wars X, Embryo clones 20 of himself inside Hysterica (technically 21 but Ange kills one in a cutscene beforehand). Fortunately, they aren't difficult and can be a really great source for money and experience for characters lagging behind.