During the Buster Call on Enies Lobby in One Piece, a horde of Captain-ranked Marines attack the Straw Hat pirates. Since Authority Equals Asskicking, each one has their own super powers, ranging from being a giant with an axe to the ability to rust metal with a touch. All are dispatched quickly despite the diversity of power.
Near the end of the first season of Gundam 00, the newly-formed UN-alliance between the three power blocks starts fielding the GN-X mobile suit. Said mobile suit has the mass-produced engine of the Gundams, enabling them to go toe-to-toe with the Thrones and actually defeat the protagonists in the final battle. Of course, by the next season they are obsolete against the new Gundams; even the newer GN-XIII is merely a mook.
The Metal Coolers in Dragon Ball Z : The Return of Cooler. Unusually for this trope, a single Metal Cooler is much stronger than any of the protagonists, dealing out curb stomp battles to a Super Namek and two Super Saiyans. In fact, depending on when this movie is supposed to be set, a single Metal Cooler is on par with the first or third forms of Cell.
In Smile Pretty Cure!, the Bad End Pretty Cure are the Evil Knockoffs of the Pretty Cures, created by Joker. They are introduced in the end of episode 45 and are killed in episode 46. And what kills them? By the new, upgraded individual attacks of the Pretty Cures, that couldn't finish the Hyper Akanbes before.
The said Hyper Akanbes are at least tougher than the Bad End Pretty Cures, but they are only Elite Mooks.
The Gamorran supersoldiers, and later Dr. Krigstein's goons, in The Authority.
The Prime Sentinels during Operation: Zero Tolerance in X-Men
The terrorist organizations at Marvel Universe sometimes do this to their men. Pym particle and Hulk-powered HYDRA mooks were part of Viper's latest world domination plot, alongside Norman Osborn. But they don't get to do much aside from thrashing jeeps and helicopters belonging to an US diplomatic mission sent to negotiate the release of Captain America, who had been taken hostage.
In Savage Dragon, there is a superpowered gang of roughly two hundred members called the Vicious Circle. Usually, they fight the Dragon en masse. It's usually not enough to beat him unless they use their elite members.
Star Wars: Legacy Darth Krayt had a secret army of Sith Troopers that can take on Sith/Jedi.
Source material notwithstanding, the ending part of the Warhammer 40,000: Gaunt's Ghosts novel Necropolis sees Gaunt and his Ghosts fight non-Codex daemons known as Darkwatchers that could teleport.
Some noble houses in Mistborn have enough allomancers to field entire strike teams of them. Though they're almost all Mistings rather than full Mistborn, they're still much more dangerous than ordinary humans would be in their place. The Lord Ruler also keeps armies of Koloss (orc-like nonhumans which are superhumanly strong and durable) but rarely uses them because while they're incredibly effective in battle, they also have a tendency to go into uncontrollable killing rages, even against allies, which makes them a weapon of last resort.
Live Action TV
At the end of Season 6 of Smallville, Lex reveals what the purpose of his secret lab called 33.1 is; to experiment on the powers of meteor-infected individuals and combine their powers into a single body as part of Project Ares. The further implementation of this plan seemed to be a mass-produced superhuman army until the main facility was destroyed in the finale by Bizarro.
The Dragon-Blooded in Exalted are essentially meant to be this. They are the weakest of the Exalted, but can pass down their powers to their children (unlike the Celestial Exalted, who exist in fixed numbers and go through Reincarnation).
Later parts of the Star Wars: Dark Forces Saga used this to add more opponents with lightsaber skills and Force powers, making them more integral to the gameplay compared to Jedi Knight, which had only offered such fights with the bosses.
The main plot of Jedi Outcast involved the Empire mass-producing Reborn troops, Imperial soldiers artificially infused with Force abilities and given lightsabers. They ranged from the basic orange Reborn, who were limited to simple lightsaber skills, to the red Reborn, who had the same Force abilities as the player (only at a slightly weaker level), to the elite Shadow Troopers, who wore black lightsaber-resistant armor and helmets (which looked like lower-tier copies of Darth Vader's own Sith armor) and had the same Force ability and lightsaber skill level as your own character, and could turn invisible.
The sequel, Jedi Academy, featured Sith Cultists who were infused with Force powers via an Artifact of Doom called the Scepter of Ragnos. The cultists were extremely specialized; some fought only with a lightsaber, some were unarmed but fought using high-level Force powers, and the rarely seen (read: less than 10 in the entire game, all in a single level) Cultist Commandos use Force-assisted jumping combined with blasters to pull off some Max Payne-like firefight action. A little later, you'd be introduced to the New Reborn, the leftovers of the Reborn from the previous game (actually there are at least as many of them in this game), who were about the same as the most powerful old Reborn, clearly superior to the Cultists.
Jedi Academy also featured elite superpowered mooks called Reborn Masters — as the name indicates, the elite among the New Reborn, and easily about as powerful as real Jedi Masters in the game. There were only a handful and they would have counted as bosses if they weren't nameless and placed at only somewhat critical junctures. They had seemingly been designed to be as difficult to beat as possible, possessing every Force power at highest level except for those limited to the player, superior lightsaber skills, and AI that made the other enemies look like idiots — you wouldn't catch a master trying to fry you with Force lightning while you were protected against it, nor would they let you jump on their heads Mario-style without retaliating, although at least they couldn't slice off three of your limbs in one go.
The Force Unleashed featured the Emperor's Shadow Guards, black-armoured warriors who wielded lightsabre-halberds and attacked with a variety of powerful Force abilities. Just one of these guys constituted a whole miniboss battle. Worse yet, they were always accompanied by cloaked Shadow Stormtroopers, who would conveniently phase in and start shooting at you just when you had the Guard on the ropes.
Many Castlevania games feature enemies, usually skeletons, who wield whips in the same manner as the Belmonts'. They tend to be up there on the threat scale compared to most enemies.
In Time Shift, the player has the ability to slow down or stop time (while continuing to move at normal speeds themselves), allowing them to slaughter basic Mooks left and right. The enemy army's trump card were the Quantum Guards, cyborg soldiers equipped with similar time-bending abilities as the player (Flash Guards could slow time and thus move at super-speeds, Storm Guards had impenetrable energy shields, and Warp Guards could teleport around by stopping time).
In Project: Snowblind, General Yan Lo's Elite Guard have the same nanoaugmented powers as the player character. There are 3 different types of Elite Guard, each one has 1 of the player's nanotech powers... 1 type can move at super-speed, 1 type has a full-body energy shield, and 1 type is equipped with a cloaking device (although, due to A.I. issues, they mostly just use the cloaking device, which is by far the least useful of the 3 powers). The General himself has all 3 powers, although he's nice enough to only use them one at time (with his boss battle being split into 3 different phases, with 1 phaser per power).
Crysis had North Korean Nanosuit soldiers, whose Nanosuits gave them the same superpowered abilities your own character had (increased durability, a recharging energy "shield" reactive armour, regenerating health, a cloaking device, and super-strength for enhanced punches and jumps). While Nomad quips that they're "just cheap knockoffs", they're actually pretty much identical to your own suit, other than a lack of speed mode and fairly average enemy A.I.
In the F.E.A.R. expansion pack Perseus Mandate, you fought against Nightcrawler Elites, who had the same Slo Mo ability as the player (which they used to zoom around at superhuman speeds in short, split-second bursts).
In Far Cry Instincts: Evolution, you face off against native Feral Warriors, who possess the same Feral powers as the player (which mostly involve enhanced jumping ability, enhanced speed, and a really mean melee attack).
In Halo, the player's only actual "superpower" that distinguishes them from the standard disposable Redshirts is a regenerating energy shield. The alien enemy officers, known as Elites, have the same regenerating energy shield as well as similar health/durability compared to the player.
The Spec Ops Elites have optional active camoflage, in addition to the ability to throw grenades. And the strongest of the Elites, the Ultras, have extremely strong shields and armor, recharge their shields much faster than others, usually have Guns Akimbo, and carry a plasma sword as a secondary weapon.
Also the Ranger Elites, who have jetpacks, Jump Pack Brutes, and Brute Stalkers, who also have stealth camo.
In Halo: Reach, the higher-ranking Elites such as Ultras, Zealots, and Generals can use the same armor abilities (e.g. Armor Lock) as the player; the latter two bordering on Boss in Mook Clothing.
Oddly, this is both used and averted in BioShock. While the background fluff describes Splicers using the same Plasmid abilities that the player can use (e.g., Incinerate! to set people on fire), in the actual game many Splicers are mostly limited to normal weapons, such as clubs, guns, and makeshift grenades. Early exceptions include the Spider Splicers, who seem to have some form of enhanced speed and agility, then Houdini Splicers, who can throw fireballs and teleport. Later chapters include Thuggish (melee) splicers acquiring a passive version of your electric attack, Houdini splicers occasionally employing a version of your Winter Blast plasmid, and the final boss (who throws various Elemental Powers projectiles).
Given that most of the splicers rather overdid things and went off the deep end it isn't totally surprising they just charge at you in a berserk rage.
Meanwhile, Bioshock Infinite has Firemen and Zealots of the Lady, who use the Devil's Kiss and Murder of Crows Vigors against the player, and are immune to the same attacks.
City of Heroes has many arguable cases, but a clear example are Crey's Paragon Protectors, who are clones of dead heroes.
In Mirror's Edge, you spend most of the game being pursued by slow but heavily armed cops and SWAT soldiers. You then learn that the bad guy's master plan is to train Ninja Parkour Cops to chase and eliminate Runners at their own game. You face off against these Ninja Parkour Cops in a few of the later levels; they have the same Le Parkour skills as your own character, allowing them to pursue you across the rooftops in ways the standard cops are incapable of.
You can find almost the exact same pattern in Mark Of The Ninja, minus the Parkour references. You spend most of the game fighting regular soldier-type rank and file guards and, occasionally, more badass elite guards, and then you face the result of 's master plan, which is evil elite high-tech ninjas who have more or less the same aptitudes as yourself.
Ace Combat has antagonist ace squadrons who in their first appearance (at least on a first or fresh playthrough) are "boss-level" pilots flying endgame planes before they're unlocked for the player. Fortunately, if they're not invulnerable, you get plenty of points for shooting them down, regardless of difficulty and even if you're by now using the same or better planes.
Most enemy types in the later Wizardry series pick up spellcasting or other special abilities as you encounter higher-level varieties, which results in fire-breathing crows and psionic robots, among other things.
In Metroid Prime, the Space Pirates that copied your beam weapon technology could be considered this. Especially since, even though they had weapons basically equivalent to yours, but eliminating the slow rate of fire you had for most of them.
The unit of engineered psychic soldiers encountered close to the end of Second Sight. They can use almost every single power that the protagonist has earned over the course of the game- largely because the stem cells used in their creation were extracted from both the Zener Children and the aformentioned protagonist, John Vattic. Interestingly enough, after you kill every last one of them, the Big Bad reveals that not only were the soldiers just one unit of several hundred spread across the United States, but the reason Vattic met them in the first place was to measure the strength of his powers, to justify using more of his cells in the next generation.
The five "Special Infected" super-zombies from Left 4 Dead. More than the usual "berserk feral ex-human trying to tear your face off", they get extensive mutations that give them long razor-claws, a tongue like a flying-catching lizard, a bladder of disorienting bile, or muscles that make them the size of a car.
Super Mario Bros. 3 had the fire-shooting Hammer Brothers that only appeared twice in the entire game; as a pair on the World 2 map, and as singleton in a World 8 Hand Trap stage. And fire-spitting Nippers in one level of World 7.
Super Mario World had Super Koopas—unshelled Koopa Troopas with Superman-style capes that let them fly. One stomp made them lose the capes and revert to normal.
Prototype gives us Hunters and Blackwatch Super Soldiers who have similar powers to Alex, in contrast with the base Infected who are all punching bags and standard Marines or Blackwatch troopers who only have weapons but no innate powers.
The Nazi Scribes in Wolfenstein fulfill this role, using a variety of Veil powers similar to those of the players, such as bulletproof shields and super-speed.
The Veil Assassins also count, though to a slightly lesser degree; they can also use the Veil, but not in as many ways as the Scribes.
inFAMOUS had conduits, Elite Mooks armed with powers similar to whichever boss they happen to work under. The first set can teleport and create a traveling explosion. The second set are either heavily armored guys who spawnankle-biters while launching rockets at you or guys who can telekinetically build a giant mecha suit out of debris. The third kind have cloaking or the ability to project a giant ghostly figure around themselves.
Likewise, Infamous 2 has the Vermaak 88, an entire army of mass-produced Conduit supersoldiers manufactured by the Big Bad, all equipped with a weakened portion of Kuo's power stolen from Kuo and transferred to them en mass.
By ASSUMING DIRECT CONTROL, Harbinger in Mass Effect 2 can turn any of its Collectors into one of these. The Eclipse Vanguards have similar abilities to possessed drones (throwing balls of biotic energy and casting a damage absorbing barrier), but their barriers and attacks are much weaker and they lack his exploding fireballs and melee attacks. Numerous biotic enemies in the first game would also possess Throw and Warp, and in the case of Asari Commandos, Throw, Stasis, Warp, and Barrier.
Gears of War features Theron Guards, enemy elite units who chant ominously, wear an enemy variant of a Badass Longcoat, and wield one-kill Torque Bows. The first time you meet them, they outnumber your squad and are already dug in. Expect to die a lot.
The Dai Li, of Avatar: The Last Airbender , are "The Secret Police" of Ba Sing Sei and prove to be some of the most formidable advisaries the gaang has to contend with. In the "Lake Laogai" episode, not only were they able to hold their own versus the gaang and Jet's group, in "The Day of Black Sun pt.2", a lone pair of Dai Li agents were able to stall Aang, Sokka, and Toph, by themselves!
The third season's Big Bad, Brother Blood, builds a small army of copies of Cyborg, which turn out to be some of most effective mooks in the series along with Mad Mod's giant nutcracker soldier robots.
All of fourth season Big Bad Trigon's mooks are also superpowered demons. These die fairly easily, all told—too bad there's a literally endless supply of them...
Near the end of Justice League Unlimited, Cadmus sends Galatea to attack the Watchtower with an army of Ultimen clones. Although the original Ultimen had a fair amount of characterization, it's implied that the mass-produced clones have more rudimentary mental conditioning.
In the Young Justice episode "Alpha Male", the Brain uses Kobra-Venom infused animals to guard his base. These include elephants, crocodiles, vultures, monkeys, and wolves injected with a serum that makes them larger and gives them Super Strength. Fortunately the Team learns that destroying their inhibitor collars frees them of the Brain's mind control and renders them neutral.