Fairy Tail has Yomazu and Kowazu. The dark guild, Grimoire Heart, is lead by Hades with seven established lesser bosses who oversee the many Mook soldiers associated with Grimoire Heart. Yomazu and Kowazu however, are in between. They're strong enough to be classified higher then a Mook, even having established names, but not strong enough to be standing alongside the leaders. They beat up Gajeel and Levy before they are defeated by them. However, Gajeel is so injured, he's Put on a Bus until Hades' defeat.
In One Piece, near the end of the "Enies Lobby" arc, Captain level Marines attacked the Straw Hats at the Bridge of Hesitation. The Straw Hats had spent the rest of the arc taking out several thousand standard Mooks, as well as fighting the government's resident assassin team, CP9 so these Elite Mooks did pretty well against the worn out Straw Hats. Still got their butts handed to them, though.
One of them scored a victory for mooks everywhere when he actually managed to destroy one of Zoro's swords. Usopp ended up sniping him down, but his actions left Zoro unable to use his strongest techniques for most of the next arc.
The Sorting Algorithm of Evil is justly used here, as well. The more and more "dangerous" the Straw Hats become, the more and more stronger marines they're gonna send out. When before, fighting a captain or commander could be the Big Bad of an arc, they're now just Elite Mooks for Luffy and the crew...except Smoker, who's more of a Boss in Mook Clothing. Throughout his time as a captain and a commodore, he's still handing Luffy his butt solely from the benefits of his Logiapowers.
Akuma of D.Gray-Man have levels, so that every time the exorcists get strong enough to Red Shirt-ify the current strongest akuma, they can just introduce a new strongest type.
The Espada from Bleach all tend to have a few lesser Arrancar that they keep around to serve this purpose, called their Fraccion. And frankly, the Big Bad considers all Arrancar to be this, at best. In the end, he considers them to be plain old Mooks after almost everyone but Harribel dies without killing a single shinigami.
Harribel's Fraccion fit this trope best of all. Why? They're by FAR the most effective of ANY Fraccion shown. While most of the Fraccion are defeated by, at best, the Number Twos of the various Gotei divisions, Harribel's trio manages to take out a grand total of FOUR Lieutenants (Matsumoto, Hinamori, Shuuhei, and Iba—in that order, and Kira was next) by summoning their pet Giant Mook. It took the Commander Generalhimself to get fed up and take them out.
The red armoured Rublum forces of the Empire in Tears to Tiara. They hand the protagonists their first real defeat in episode 8, though that was due in part to Arthur's lack of strategy beyond "charge them and hope for the best". Well, they used logs too, but the Rublum soldiers just got back up after being hit by the logs.
The giant mecha in the festival arc of Mahou Sensei Negima! had their weaponry quietly upgraded to no longer fire mere stripper rays. Apart from that they were indistuinguishable from their predecessors.
Hotel Moscow in Black Lagoon has the Desantniki (who are called the "Vysotoniki" by Dutch), Balalaika's personal bodyguard and inner circle made up of former USSR paratroopers that fought under her in Afghanistan.
In Vinland Saga, the viking kings call upon the Jomsvikings, a mercenary band for hire made up of war veterans, for elite muscle. Outside of fighting named characters with Character Shields, they're pretty much unstoppable.
Though the original was introduced as an individual case of A.I. Is a Crapshoot and eventually transformed into the recurring villain Bastion, later X-Men stories have made the Nimrod type of Sentinels this in relation to the usual versions.
Intergang itself sometimes has elite mook squads of its own, like the "Wall Crawler" assassins seen in some Superman stories.
In the Marvel Comics Universe, the original Power Broker's business involved selling super-strength upgrades, often to villains looking to assemble Elite Mook units. The Broker himself employed a squad of such called the Sweat Shop.
Another Marvel subversive group, Advanced Idea Mechanics, started as the Elite Mooks of HYDRA (aka THEM), being its super-science division; AIM itself mass-produced synthetic soldiers like its "chemical androids" and Adaptoids. HYDRA itself developed robotic soldiers called Dreadnoughts for this purpose, and in some continuities HYDRA itself started out as or becomes the Elite Mook organization working for the Red Skull.
For more conventional criminals like Spider-Man and Daredevil archfoe the Kingpin of Crime, the Hand frequently serves as a group of killers and enforcers a cut above the average mob wiseguy. The Hand usually has its own plans, though. Unsurprisingly, the Hand and HYDRA share a history and have alternately served as elite mooks for one another on separate occasions.
Later, a group of generals sends a special forces squad after Frank precisely because they're the Army's elite.
Manute from Sin City had a squad of mobsters under his command but he sent a group of former IRA mercs to fight Dwight and the Old Town girls. They did a good job of it due to a lot of firepower and one managed to briefly catch Miho off-guard but they were all eventually defeated.
The SAS in ARSENAL are called in by SEELE to help Nightshift Bunnies Aoi Mogami, Kaede Agano, and Satsuki Ooi do battle with a Shinji Ikari-controlled NERV. They are slaughtered wholesale by Misato Katsuragi, Touji Suzuhara's younger sister, and Pen-Pen.
The Assault Troopers from The TSAB Acturus War, who are both mages and conventionally-trained special forces. We see only four named ones on-screen, but they do fairly well considering they end up fighting Nanoha, Fate, Vita and Signum.
The Immortal Game has the Unicorn puppets, which, due to their magic, are greater threats than the Earth pony and Pegasus puppets.
The Shadowbolts (formerly the Black Ravens) serve as this to Nightmare Moon.
Films — Live Action
300 applied Action Movie tropes to historical events, including making the Persian 10,000 Immortals Elite Mooks.
Agents of the East India Co. in Pirates of the Caribbean: Dead Man's Chest. We only see one of them (Mercer) but Jack "vanished from under the eyes of seven agents of the East India Company" and this is listed as an impressive feat.
The Uruk-Hai in The Lord of the Rings movies, though after their introduction they don't seem to pose much of a problem.
The Super Battle Droids and destroyer droids (droidekas) in Star Wars: Attack of the Clones.
General Grevious' Magna Guards, non-Jedi droids who are able to fight against Jedi in melee combat and do relatively well (i.e. live longer than about 6 or 7 seconds).
The Royal Guard, the guys in red, are supposed to look like elite mooks, at least. They don't do anything in the original series and get curb stomped by Yoda in the prequels.
The Expanded Universe gives us Darth Vader's 501st Legion (named after the fan club), stormtroopers who can actually shoot straight. Justified because canonically, the Legion remains composed purely of clone troops and not ordinary recruits.
At the end of Batman Begins, Ra's Al Ghul sends 4 serious-looking ninjas in full metal body armor to fight Batman. They do marginally better than everyone else who's tried to fight Batman up to this point until they pushed him into a mob.
Both Equilibrium and Ultraviolet feature the hero battling a group of several unique-looking Mooks armed with katanas, just before the final fight with the Big Bad. These guys are either Elite Mooks, or complete idiots, for fighting only with swords in a world where everyone is equipped with automatic weapons. In any case they don't do noticeably better against the hero than all the previous Mooks...i.e. they all get killed in about 6 or 7 seconds.
In The Matrix Reloaded, this is the excuse for Neo still having to get into martial arts battles with the Agents, despite apparently transcending hand-to-hand combat at the end of the first film. After an exchange with the new agents, we says, "Hmm, upgrades!" The agents don't actually seem to be any tougher than the previous set in comparison to anyone else.
In Inception, this is the difference between an untrained mind's projections and a trained one. Normally, a mind's subconscious projections take on the form of waves of mindless civilains that swarm intruders in the dreamworlds, while if a mind has been trained to resist intrusion, the projections are armed with heavy weaponry and attack in coordinated groups.
The Cardinal's Guard in the 1973-4 film versions of The Three Musketeers probably qualify. Although the novel depicts them as more or less equal to the king's musketeers in training and prestige—and in the first fight sequence the musketeers hesitate before taking them on at 1-2 odds—by the final fight sequences, the heroes are dispatching them by the dozen.
The Black Demon Ninjas from Violent Shit III: Infantry of Doom.
In The Expendables, there is General Garza's special forces, identified by their red berets, jungle camouflage, and green-and-yellow facepaint. They actually live up to their reputation as well, forcing the Expendables to seriously work to kill them, unlike the regular soldiers who they mow down with regularity.
Source material notwithstanding, the Warhammer 40,000: Gaunt's Ghosts novels after Necropolis had them fighting the Blood Pact, the retinue of the Chaos warlord they were fighting against, who were supposedly better than the generic heretics and zealots that came before. The Guns of Tanith also introduced Loxatl mercenaries that could take lots of lasfire.
The Steel Inquisitors in Mistborn. A little more elite than most Elite Mooks, in the first book only Sazed and Kelsier can take them on and live, and it's still not very advisable. Kelsier killing one is treated like him snatching the sun out of the sky: everybody around falls still and can't believe their eyes. Oh, and they have literal Spikes of Villainy...through both of their eyes.
Hazekillers (who are warriors specially trained to kill allomancers), and koloss are Elite Mooks who are more powerful than regular Mooks, but less powerful than Inquisitors.
In Cerberon Wizard Royal Elect Tmneal Kravat has a group of half-hackal warriors called the Nine Fangs explicitly described as elite soldiers. Their eliteness seems more like an Informed Ability when Aladavan fries them with a massive ball of lightning, and decapitates the blinded and severely burned survivors who are still trying to achieve their objective despite their fatal injuries.
The ur-viles from the Chronicles Of Thomas Covenant are an interesting example. They're no stronger than the stock mooks, Cavewights (who are physically powerful but weak-willed), but are far more dangerous because they're smarter (Cavewights will just Zerg Rush the enemy; ur-viles always fight in disciplined formations) and possess potent magic (ur-vile loremasters, their primary magic-users, can cause even experienced warriors to freak when they show up).
Mighty Morphin' Power Rangers did this regularly, with So Last Season existing before the changing-teams-every-year phenomenon, with each set of Mooks being considered "elite" as compared to the last, until reaching the standard Mook success rate about five episodes in. Z-putties are elite until the Rangers find out they can just hit the big giant Lord Zedd Z symbol on their chests and the Putties will lose power and shatter (though the fights still last a while because it has to be a hard direct hit). Then Tengas were elite until...they weren't. Power Rangers Zeo's Mecha-Mooks, the Cogs, were equally hyped and actually tougher than Putties or Tengas...but that just meant the Rangers had to actually suit up to fight them. Rita also had a short-lived line of Super Putties who were tougher, stronger, and would pull a starfish and regenerate into two Super Putties if smashed, which forced the Rangers to retrieve special blasters in order to break them. These were not used again because Rita had only so much of the special clay used to make them.
In VR Troopers, there were Skugs and eventually the stronger Ultra Skugs. (Ultra Skugs have the same Weaksauce Weakness, though: if two touch, both disintegrate.) Masked Rider has the Maggots (comic relief stooge villains, used for jobs like distraction and MacGuffin theft) and the Commandoids (used to fight.) Kamen Rider Dragon Knight has three stages of grunt evolution (red normal Mooks, white stronger Elite Mooks, blue flying super-Mooks.)
The Kull Warriors in Stargate SG-1 are — watch this — Anubis' Frankenstein's symbiotically enhanced super-zombie cyborgImplacable Men. One episode of SG-1 also showed that some of the Jaffa under Anubis were elite Ninja Jaffa. For some reason, they never showed up again after that episode. Sokar had the Red Guard, who were more heavily armored and fewer in number than the usual grunts. Apophis used them after knocking off Sokar and taking over his territory.
Star Trek: The Next Generation plays with this concerning the Borg. The Borg start out as chump Mooks. The problem is...once you knock off a few of the chump Mooks, ALL of them become Elite Mooks, or at least elite enough that they can kick your ass. New foe, wash, rinse, repeat.
Season 7 of Buffy the Vampire Slayer has elite vampires called Turok-han. The first one to make an appearance is actually incredibly dangerous, but once a whole army of them are released at once, they go down easily.
Nikita: Division has several ascending levels of Elite Mooks:
The Cleaners, described by Owen as being stronger and faster than regular agents, and who "clean up" after Division's missions.
The Reapers, Cleaners trained to deal with other Division agents.
And the best of the best are chosen to act as Guardians (like Owen), who protect Percy's black boxes.
When the evil Queen sees Captain EO changing her zombie guards into 80's dancers with his music, she sends in scary robots with electric whips to stop him. The robots are immune to his music and the rainbows he shoots out of his hands.
Elites choices in Warhammer 40,000, which are Exactly What It Says on the Tin. Elite choices vary between specialized units tailored for a specific purpose, to simply better armed and more expensive versions of the army's core troops, Space Marines have Veterans, Chaos Space Marines have Chosen, Orks have nobs (elite boyz), Eldar have Dire Avengers (elite guardians), Dark Eldar have Trueborn (elite raiders), Necrons have Immortals (elite warriors), and so on and so on. All the Chaos Gods have daemons like this.
From a fluff perspective, All Space Marines qualify compared to the Imperial Guardsmen and PDF Forces who do the bulk of the Imperium's fighting. The Eldar Aspect Warriors also perform similar roles for their people.
Special and Rare choices in Warhammer. Every army has at least one unit that is effectively one unit of normal infantry, just better trained, better equipped, less likely to run, Spikes of Villainy for the evil races, and with a badass sounding name. Compare Chosen to normal Chaos Warriors, Stormvermin to bog-standard Clanrats, Phoenix Guard or White Lions to ordinary High Elf Spearmen...etc. The more intimidating the name, the faster you have to run away from them.
Shadowrun has, among other things, Aztechnology's Leopard Guards, Ares Firewatch Teams, and Renraku's Red Samurai.
Most common monster races for mooks have an elite mook variant. Gnolls have the nunchuk-wielding flinds, goblins have the militaristic hobgoblins and bullying bugbears, lizardfolk have the fiendish Lizard Kings, and orcs have numerous variations.
Any mooks that don't have prebuilt variations can just be made into Elite Mooks by the DM by adding class levels or templates, seasoned to taste.
4E breaks monsters down into tiers of elite-ness. Minions minor mooks who are just like regular monsters, but die in one hit. Elites are monsters that are somewhat harder than their baseline versions, usually lending to using them as leaders. Solos are double-dose Elite Mooks designed to stand on their own against a whole team of players.
The Bohrok-Kal in BIONICLE. The ordinary Bohrok rely heavily on Zerg Rush to overwhelm their foes. But there are only six Bohrok-Kal, who have unique powers, are intelligent enough to speak, and Dangerously Genre Savvy enough to steal the icon that is the source of the Toa Nuva's powers in order to render them inert.
Ridley's "Ninja Space Pirate bodyguards" in Super Metroid.
Literal elite monsters in the Diablo series, which was handed down to its spiritual successor World of Warcraft. They have a golden border around their portrait and are much tougher than their normal counterparts. How much more depends on the setting. Outdoor elites might be killed by a single character of the same level, although it's much more difficult, while dungeon monsters are designed to be a threat for a full group or even a raid (up to 40 players).
The obscure Macintosh Wolfenstein/Doom clone Sensory Overload had, in its later levels, elite guards who looked like Nazi officers and wielded machine guns, and cyborg soldiers who talked like Darth Vader and threw plasma balls(the same projectile as the Electrogun). The unnamed female Dragon and Final Boss was a slightly enhanced(faster, and with a melee attack) Palette Swap of the cyborgs, ie a type of King Mook (or queen mook, if you will).
Combine Elites in Half-Life 2, who wear white uniforms instead of the grey and black variety found in others, and have weapons with an "alternate fire" mode which can instantly disintegrate NPCs, whether Red Shirt or Mook, are a mixed bag. In-Universe, they are a straight example, but in gameplay terms, they're closer to Fake Ultimate Mook: the dreaded pulse projectile only deals 15 damage to Gordon, they can't throw the grenades the ordinary Overwatch soldier is known and feared for using, and their health is negligibly higher than normal Overwatch.
Ninja Gaiden, which places Bad Ass super-ninja Ryu Hayabusa and Fiend-Hunter Rachel in the Vigoor Empire with the task of killing everything around them. The game expands upon the genre staple of tough, then tougher, than tougher monsters by arranging a pattern of leadership for all enemies, human, fiend, and mechanical.
The Elites of Halo, the strongest form of which are the gold Zealot and the black (violet in 2) Spec-Ops types, the latter of which show up in the last two levels of the game. Both have a ton of shields and armor, have more advanced agility and AI, and Blacks can use grenades unlike other elites, particularly annoying on The Maw. They are accompanied by the Spec-ops Grunts, which often carry Fuel Rod Cannons.
Ultra Elites, aka silver or platinum elites, which are ubiquitous on Legendary. They have much stronger shields and more health than other Elites (e.g., can take four or five sniper shots to the head), regenerate their shields much faster, often have Guns Akimbo, and can go berserk and wield instant-death Energy Swords.
Also introduced are Heavy and Ultra Grunts, experts with grenades and BFGs, and the jetpacking Ranger Elites.
The most powerful Brutes are Brute Chieftains, who are heavily armored, can't be stuck with grenades on their armor, wield Gravity Hammers or fuel rod guns, are equipped with temporary invincibility shields, and can also take about three grenades to the face before dying (and that's if you're not killed when they go berserk when their armor comes off). Other elite mooks include Brute Captains, Brute Bodyguards, which replace the Honor Guards, and Jump-Pack Brutes.
The Sacred Icon and Quarantine Zone levels have Sentinel Majors, gold Sentinels which have shields and more powerful blue beams.
Of course, the strongest of all Sentinels are the Enforcers. These are Sentinels the size of tanks with frontal energy shields, rapid-fire pulse beams, mortars, and pincers for destroying any hapless vehicle that happens to get stuck under it. Even tanks.
Halo: Reach has two additional Elite ranks, the General and Field Marshal.
Halo 4 has the Promethean Knights, which are more powerful than the rest of the Prometheans, can teleport across the field, armed with tougher weapons, and can be revived by Watchers.
In God Hand, there are two basic elite types: the "tall" model and the "fat" model. Both are much harder to send flying and have a lot more health.
Tom Clancy's End War has them. How? The player's army, stated to be the best taken and bunched up from all the other elite forces of their root military, and The Cavalry commonly in other circumstances.
The geth of Mass Effect start off with your regular geth soldiers, but as the game progresses, geth shock troopers start showing up, and then you start getting meaner variants, like Juggernauts, Destroyers, and the pants-browningly potent Primes.
Cerberus has this in the form of the Nemesis and Phantom units, elite specialists designed to work perfectly in tandem with one another: while one keeps you pinned down with the threat of sniper fire that can instantaneously destroy your shields, the other closes the distance so they can insta-kill you with their fancy swords. Phantoms also have the benefit of crazy-powerful handguns that can kill you long before they close the distance if you don't take cover, in addition to cloaking devices and fancy acrobatics. Also, the Atlas. Very tall, very strong, and very dangerous.
Many Metal Gear games have several elite enemy soldiers in addition to the regular kind fought by the player throughout the course of each game.
The original Metal Gear Solid have the Heavily Armed Troops, who wear full body armor and helmets. They are specifically said to be former members of Big Boss' elite guard (rather than VR-trained novices like the rest) and thus they have more hit points than the other troops.
Metal Gear Solid 2 has the Hi-Tech Soldiers, who are members of Solidus Snake's private guard and appear only during the alert phase during the latter half of the Plant Chapter (specifically after Raiden contacts Ames). Later, when the player reaches Arsenal Gear, they'll encounter the Tengu Commandos, who are armed with ninja-like gear.
Heavy Armor troopers in Army Of Two, who are immune to most gunfire from the front — though grenades and rockets can hurt them, and a well-placed shot with a sniper rifle can knock them down, allowing one to snipe them between the legs.
The Vanguard beastmen in the Dynamis regions of Final Fantasy XI. The Kindred demons probably also count for the Beastmen hordes as a whole, story-wise.
In the series in general, Behemoths are always among the strongest random encounters. Bosses and mini-bosses sometimes take the form of a recolored Behemoth or the behemoth itself can be one (and turn into a random encounter later).
Deus Ex featured Men in Black agents, who mostly carried auto-shotguns, could survive more than 3 times as much damage as standard Mooks, and who exploded when killed.
The sequel Deus Ex: Invisible War had Illuminati Elite for the Illuminati faction, who looked like Mr. Freeze, carried railguns, and released clouds of poisonous gas from their corpses after dying. The opposing Templar faction countered them with Powered Armor Mooks equipped with rocket launchers.
Deus Ex: Human Revolution has Belltower Spec-Ops, who wear red and black, and come in four different types: Soldiers, who are just slightly tougher than normal Mooks; Sneakers, who wear helmets, have mechanical legs and have Cloak augmentations; Shifters, who act as Snipers; and Ogres, massive soldiers who can take tons of punishment, wield miniguns, and have Typhoon augmentations.
Mexican Army Elite Mooks appear in Tom Clancy's Ghost Recon: Advanced Warfighter, in the form of Aguila 7 Special Forces soldiers. Realistically, although they're better trained and equipped than standard infantry, they still go down after a couple assault rifle hits.
Story-wise, some of the terrorists in Tom Clancy's Rainbow Six: Vegas are ex-Special Forces mercenaries, while others are simply Mexican criminals working for Irena Morales. However, in-game, there's no actual distinction between the groups, as they both use the same set of character models and uniforms, as well as the same A.I. and equipment.
The second-to-last level in Splinter Cell: Chaos Theory ended with Sam up against Shetland's personal bodyguards, about 8 elite Displace Mercenaries equipped with facemasks and thermal goggles. These used to be the only enemies in the entire series who could see you in the dark (some enemies in the series, i.e. the Georgian Special Forces from the final mission in Splinter Cell, wear night-vision goggles, but still couldn't see you in the dark unless you move or are very close). Then came Conviction and the enemy Splinter Cells, who had sonar goggles that let them see Sam's Last Known Position through darkness and cover.
Gears of War has Theron Guards, who are faster, smarter, and tougher than standard Locust Drones, and are also equipped with One-Hit Kill Torque Bows.
Gears of War 3 has the Armored Kantus, the elite version of Kantus, who duel wield gorgon smgs, have a powerful rolling attack, and can only be harmed either by explosives or by shooting them in the mouth when they shriek to heal wounded enemies.
In F.E.A.R., Replica Elite soldiers, wearing black uniforms and white hockey masks, show up in one of the game's final levels. They can survive more bullets than standard Mooks, but several carry BFGs.
The Replica Heavies, tall heavily-armored cyborgs who carry Penetrators, Particle Beam Guns, or other BFGs. Slow but lethal. Can be a Boss in Mook Clothing.
Crysis actually has 2 kinds of Elite Mooks. North Korean Special Forces are simply regular Korean soldiers with better accuracy and equipment, whom you probably won't even notice unless you're looking for them (they wear dark armor, black facepaint, and have laser-sights). There are also a handful of North Korean Nanosuit soldiers, who wear the same superpowered Nanosuits that the player does. Enemy Nanosuit soldiers feature increased durability, a recharging energy "shield", regenerating health, super-powered punches and jumping ability, and a cloaking device.
2 has the Commander variants of Grunts and Stalkers, who have "shields". Guardians are King Mooks since they only appear in one - specifically the last - encounter.
3 has CELL Enforcers who wear heavy armour and wield machineguns or Grenade Launchers.
Red Faction 2 is an interesting case, as Elite Mooks are fought in the very beginning of the game(the prologue mission), and oddly disappear completely after the first few levels, where they're replaced by weaker, but more heavily armed, standard infantry. These "Sopot Elite Guards" wore metal armor and faceplates, could survive about twice as much damage as a standard Mook, and talked like Darth Vader.
Elite Mooks make a comeback in the final mission of the game, in the form of Elite Nano Soldiers.
The originalRed Factions Elite Guards, first seen in the Administration level, and later in Capek's lair and other high-security areas, had a different voice, spoke more aggressive catch phrases, moved and dodged faster and had much tougher armor than the standard Mooks, and frequently wielded BFGs.
Time Shift had cybernetic Quantum Guards, who possess the same time-bending powers as the player.
The first game had the Pharcom Elite Guards, and the second had the Agency Men in Black (instant max danger when they see you, sniper accuracy).
Borderlands gives Elite Mooks the label of "Badass" in front of their enemy type. Your first New Game+ with a character has these enemies labelled Bad Mutha, a second time labels them as "Superbad". In the sequel, they're generally known as "Super Badass" or "Ultimate Super Badass"
The Big Daddies and Houdini Splicers, as well as other special kinds, Splicers from BioShock. Later in the games, elite versions of Big Daddies can be found; they are stronger, faster, and tougher than regular Big Daddies
BioShock 2 introduces Brute Splicers, which are essentially the Big Daddy equivalent of Splicers.
GoldenEye and Perfect Dark often broke out the Elite Mooks during a high-alert situation, for example, in GoldenEye, once the Scripted Event alarm goes off after hacking the mainframes in Severnaya, endless waves of smart, quick, heavily armed elite guards are spawned (get out of there!). Near the end of the Datadyne Extraction level in Perfect Dark, Cassandra kills the lights and you have to fight her Bodyguard Babes (who have night vision goggles) in the dark, which is quite frustrating on Perfect Agent difficulty. PD also has the Datadyne Shock Troops (better health, better AI, and sometimes better weapons) and female Datadyne guards (better AI and almost always better weapons).
S.T.A.L.K.E.R.: Shadow of Chernobyl has Spetsnaz special forces soldiers and Military Stalkers, who have the two best non-exosuit armors in the game.
The general trend of late game introduction of elite mooks is subverted in STALKER - the player can encounter Spetsnaz in the first area of the game, in the Cordon by the Military Guard Post. Approximately two to three hours later, the PC can encounter them in Agroprom Research Facility if they hang too long around after rescuing Mole from the military. At both times a PC will likely have a low end assault rifle/sub-machine gun and armour, leading to a quick death if the PC chooses to fight back.
In general, within the games, any mook wearing a SEVA suit or Exoskeleton is this, reinforced with their high-end weaponry.
The Monolith faction is comprised almost entirely of these kind of mooks, since they have access to almost all of the weapons in the games, including the deadly Gauss Rifle.
Dragon Quest I's final dungeon is guarded by the deadliest, most demonic variations of the Mooks you've faced: Axe Knights, Armored Knights, Blue Dragons, Red Dragons, etc. They have high defense stats, deal massive damage, and have the most devastating spells, such as Sleep(Axe Knights have both this and Stopspell, preventing you from using your own Stopspell), Healmore and Hurtmore(the Armored Knight has both Healmore and Hurtmore). If you aren't sufficiently leveled up, you can kiss your ass goodbye here. Some of these are invincible to magic. And sometimes, the only winning move is not to fight.
The Silent Hill series features tougher, faster, Palette Swap (or not) versions of the enemies in certain areas (or when you're sucked into the mirror version of the town/area). For example the Night Flutterers (Air Screamers, but more human-like and with their faces covered in worms), Worm Heads (upgrade of Groaner, the ubiquitous zombie dogs, but with a worm for a face), and Shadow Children(transparent version of gray children) in SH 1, "nightmare nurses" in SH 2, and "advanced Closers" in SH 3.
The Ace Combat games have these in the form of the enemy aces, both individual and ace squadrons such as Yellow Squadron (04) or Strigon Team (6), who in a first playthrough will be flying better planes (until late game when the player can afford better) and are better pilots; in 04's "Shattered Skies" mission the Yellow Squadron are present but extremely hard to hit - actually landing a shot on one will trigger special dialogue and prompt them to retreat. The Mook half partially comes from the fact that these pilots are usually never individually identified (in 04whichever Yellow is shot down at Stonehenge is deemed to be Yellow 4, and Yellow 13's fate is sealed at Farbanti by the player having to shoot down all the Yellows there), but the Ace Combat 6 Assault Records has individual Strigon profiles unlock after you shoot down Strigons in certain missions.
Most enemy types in the Wizardry games start off as regular Mooks, but upgrade to Elite Mooks in higher level areas, then eventually to Superpowered Mooks. Not to be confused with the actual Mook race in the game, which are approximately high-tech psychic Wookiees.
In the Pokémon games, after going through enough Team Rocket (Magma, Aqua, Galactic...) Grunts, you may run into an Executive, who often serves as a miniboss of sorts.
Better examples are in the Pokémon Ranger games, where the original has Elite Mooks, the sequel has Mook-like Admins with higher ups, and Guardian Signs has two levels of admin.
Team Flare fits the bill much better than previous teams, as its Admins are a generic class just like grunts; it's the scientists that are unique.
A somewhat different definition of 'mook', but Ace Trainer (Cooltrainer in earlier generations) class NPCs often appear in Victory Road and other high-level areas and use tougher Pokémon and superior tactics to most generic trainers. Their Japanese name is "Elite Trainer".
Later in Valkyria Chronicles, the enemies become tougher and become labeled "Elite", the black-clad Imperial Guards even more so.
There are also additional units during the main campaign called "Aces", which are named and are tougher than the standard Imperial soldier. Defeating one in combat will allow you to get a unique enemy weapon after you win the battle.
The latter half of Mega Man X 8's final level gives us mass-produced copies of Sigma.
In the Wing Commander series, most of the games have the elite opponents either named and with personalities, flying unique ships, or both. The exceptions:
The Drakhai, in Wing Commander II. Slightly better defensive stats for their ships, and an AI set one level above the regular opponents were the primary distinguishing characteristics, aside from their specific taunt "You cannot defeat the Drakhai" (ignoring that you regularly did just that).
In addition to the few named opponents (other than Seether, which ones depended on when you defect, Wing Commander IV also had nameless, generic "ace" pilots.
In Dynasty Warriors 6, enemy generals will sometimes be accompanied by nameless Lieutenants. This can lead to the odd situation where you curb stomp the general himelf, and then immediately find yourself getting slapped around by his elite goons.
In The Chronicles of Riddick: Assault on Dark Athena, the Mercs in red armor with red googles encountered towards the end of the game are insanely well armored (taking almost a full clip of assault rifle fire to kill), but most players won't even notice since by that point in the game you're given a One-Hit Kill rifle with unlimited ammo.
Command & Conquer Generals has the USA faction comprised entirely of these. The basic infantry, air and tank units are the US Army Ranger, F-22 Raptors and M1A2 Abrams (called the Crusader in the game) and the more advanced units keep getting even better.
Battlefield: Bad Company 2's singleplayer campaign actually points out the presence of Elite Mooks in the loading screen hints before the mission Zero Dark Thirty, warning the player that they are better equipped and have faster reaction time than average troops. They show up about midway through the level, in the form of Kirilenko's green-clad personal guards. They're no more durable than most mooks, but they are, indeed, faster, and carry some weapons that are normally available only to the player.
And the SPECACT DLC lets you become the Elite Mook in MP!
The Lord of the Rings Online has signature, elite, elite master, and nemesis versions of mooks, each progressively more dangerous. Signatures can be found on the landscape; nemeses, with over 20 times normal health, are confined to raid dungeons, but are still nameless mooks.
It's not really that indicative, though, at least between Elite Master and Nemesis. The player is about equal to a signature in health(Less for some classes, like lore-masters), but are pushed up to about the strength of an elite by their advanced human brains and their much larger array of moves. A normal enemy has about 50% of your hitpoints and a swarm has about 25%. Generally, each level is about twice as powerful as the last, up to Elite Master. The line between Elite Master and Nemesis is INCREDIBLY blurry. In the first part of the Great Barrows, a 6-man instance, you fight an Elite Master who's REALLY tough, and you'll probably wipe several times. In the 6-man version of the fourth skirmish, Thievery and Mischief, you fight three nemeses at once as a boss with relative ease.
The Uncommon Commons of Left 4 Dead 2 are Common Infected (the average zombie of the 28 Days Later kind) but with perks that make them tougher than average: Riot Infected in body armour that make them bulletproof everywhere except the back, Hazmat Infected in fireproof biohazard suits, Mudmen who crawl on all fours, move quickly in water and can blind the Survivors with mud, Clown Infected whose squeaky shoes and noses attract other nearby zombies, and Worker Infected who won't follow pipe bombs/bile jars because they wear ear protection.
In Rayman Revolution, the robotpirates got steadily more elite depending upon colour scheme: from weakest to meanest, it goes green->purple->yellow->red->those idiots in barrels. (They get steadily less elite as your main attack gets more powerful, however.)
The first Soldier of Fortune had the Order Troopers, and Double Helix had the Prometheus operatives. In Payback, the Big Bad's elite minions wear body armor similar to Rainbow Six agents, and like all mooks on the final mission, inflict much more damage than in previous missions, and can easily kill you in one hit on Hard difficulty.
In Rise Of The Kasai, enemies wearing armor count as this; they're the same as normal enemies but are impervious to arrows, and take a few more hits to kill. Depending on which weapon you're using at the time and how lucky you are, "a few" can translate to "one" for a grand total of two hits.
Starcraft has elite versions of normal units, such as the Zerg Hunter Killers. These are buffed up Hydralisks with twice as much health and firepower as any normal Hydralisk.
The sequel takes this further, with mercenaries who not only have better damage and health to start with, and benefit from upgrades researched in-game, but in the single-player campaign armory and lab upgrades apply to units of the appropriate type as well, so Hammer Securities troops you pick up benefit from your Ultra-Capacitors, Vanadium Plating, Concussive Shells, and Kinetic Foam, as well as any of your bunkers' Neosteel Frames and Projectile Accelerators.
Time Crisis's red-uniformed enemies have near 100% accuracy, making them Demonic Spiders. At least you get a warning when they're about to fire in 2 and beyond. In the first game, Sherudo and Wild Dog have white-uniformed bodyguards. There are also the heavy weapons soldiers(with machine guns, rocket launchers, and flamethrowers), and the gray commandos (second to the reds) in the later games.
The Fable games have these. The first has the "Minion" monster, large armored monstrosities that can give even an experienced fighter a run for his money.
Fable II has the Spire Guards. justified, as most spire guards are either mercs hired from champions of The Crucible, or just have their memories and identity ripped apart and become unthinking brutes.
Revelations replaces the Papal Guards with the Janissaries, who are even more Kung Fu Proof by being able to survive killstreaks.
3 has the Highlanders/Grenadiers with their giant axes and ability to counter normal attacks, Knife Nut Scouts that can counter disarms or guard breakers and the Hessian Jagers who can counter almost all melee attacks.
All games from II onwards have guard types called "Elite", but ironically these are some of the weakest guards in the game (ranking only above militia).
"The walkers" are this compared to "Infected Citizens". Unlike other examples of this trope, The walkers aren't threat to Alex even in large groups.
Prototype2 has the Brawlers for the Infected, the Orions for Blackwatch, and eventually the Evolved
Guild Wars: In Prophecies, the Mursaat fill this role compared to the white Mantle. In Factions, Shiro'ken are elite mooks compared to afflicted. In Nightfall, Margonites (and torment demons to an extent) act in this role compared to normal Kournan soldiers.
The Bratgirls from Crash Of The Titans, which have a lot of health (Although the dropkick can still kill them in 1 hit) and can do a lot of damage with their attacks, especially their megaphone attack which also dizzies you. In Mind Over Mutant however, they have been significantly downgraded, not having nearly as much health and doing much less damage.
Starting with the fourth mission in Medal of Honor: Frontline, you encounter elite mooks with body armor who can take twice as much punishment as the normal mooks.
Alpha Protocol has special elite soldiers intermixed with the regular mooks. These are visible if one looks closely, as they'll have a gray "endurance" meter over their health meter and are noticeably tougher, more aggressive, and better-armed. Al-Samaad's elite soldiers are notable by their red balaclavas/scarves, while Deus Vult's elites are more noticeable by their body armor instead of generic suits or dark muscle shirts, and VCI elites can be spotted wearing berets and no balaclavas. Some of the more professional elites are harder to notice because they all wear the same uniform (CPA, G22, and Alpha Protocol agents) while others are harder to spot because they have no actual uniform (Russian Mafia and Triads).
In The Saboteur, we get the superior Nazi soldiers who uses very powerful weapons and armor. Lucky for you, you get to use the weapons too.
In Batman: Arkham City, there is a team of Elite Mooks called Tyger, which are the top mercenary group of Ex-Special Forces that were specially trained to go head to head against Batman.
Typically, the 2nd or 3rd in command of a gang in The Warriors will fall under this trope, having more health and strength than the common mook.
Borderlands have several variants of this trope, using names such as Badass, Bad Mutha, Superbad, and other names.
In most MM Os, there is some form of elite mook to keep the challenge up. Most of the time they will be either mini/sub bosses or named/colored/giant mooks, such as "Deadly spider" for a generic name that you might see, that show up at a certain place or mixed in with the normal mooks.
The Arch-Viles of Doom are Elite Mook that can summon or resurrect lesser mooks.
The Genedisruptor Parasites in Evolva. Appearing only during the two last levels, not only they are significantly larger than any other mook (to the point that their small version is about the same size than standard mooks), but they can also take a lot of damage, and their main attack is a beam that drains life fast and confuses your Genohunters (if the affected Genohunter is the one being controlled, it inverts the controls; on non-controlled Genohunters, it makes them start attacking each other).
Each enemy group in Saints Row The Third has its own particular Elite Mooks, often carrying unique weapons such as riot shields or bomb launchers.
The Syndicate gangs will also throw out Brutes. Brutes are big hulking bruisers that take a lot of damage to kill, can do a lot of damage, and can flip cars and obstacles around with ease. They can also potentially come armed with miniguns or flamethrowers.
Throughout all the Saints Row games, your named Homies can be this, as they're generally tougher than random Saints members picked up off the street. In The Third you also get a Brute of your own in Genius Bruiser Oleg.
The Terran State in X3 Terran Conflict has the AGI Task Force (ATF) Elite Mooks. The ATF have their own fleet of entirely unique ship designs, carry ridiculously powerful missiles for their missile frigates, and ATF ships will never bail out or surrender. Other races typically have their plain "Military" ships making up their Elite Mooks - if you were to attack the Boron, for example, you'd mostly be attacking their poorly armed Police and Border Control ships before the military shows up with much better equipped ships.
Resident Evil 4 has the Ganado Militia, which inhabit the Final Dungeon and are more intelligent, faster, and better armed, some wielding large hammers, rocket launchers, or Gatling guns.
Dark Souls has the Balder Knights (also known as Elite Undead Soldiers) starting from Undead Parish. While most Undead Soldiers you face so far aren't much of a threat, Balder Knights intend to shock newbies into a much more careful playing style, as the swordsman-type Knights wield their iconic Balder Shield with rapid attacks from their Balder Straight Swords, while Fencer-type Knights are even faster, and is able to parry you, with usually disastrous consequence if they do. In NG+ onwards, stories of Balder Fencers one-hit-KO-ing experienced, but careless players abound.
Hollow Undead are even more of a pushover, especially past the first few levels. Come to Duke's Archives, and you'll be greeted with Crystallized Hollows. Heavy defense against physical attacks, nigh-invulnerable to magic, and usually backed up by Status Buff-capable Channelers, themselves an example of Boss in Mook Clothing. Due to the narrow walkways of the Archives, getting sniped by a powered-up Crystal Hollow Archer can instantly kill you, especially when you have your back exposed from fighting others.
P.N.03's Pilz, the most common mook, have several palette swaps, each tougher, more agile, and more intelligent than the previous. Additional sub-variations are armed with missile launchers or plasma cannons.
The rare Nightmares in Kingdom Hearts 3D are simply a white Palette Swap of the usual nightmare types, but have much higher stats, to the point where it's tough to cause more then Scratch Damage to them initially, plus they can always take a sizable chunk out of your health, even if you're considerably higher in level then them.
No More Heroes 2: Desperate Struggle has one type for the fat mooks. Chainsaw-wielding fat mooks can take a lot of punishment before they flinch and can carve huge chunks of health out of Travis' life meter.
The regular, non-Behemoth Super Mutants in Fallout 3 come in three kinds: Super Mutant, Super Mutant Brute and Super Mutant Master, each one with ascending HP and weapon capabilities respectively. Plain Super Mutants aren't armored, Masters are all armored, and Brutes are both armored and unarmored. Broken Steel adds a fourth rank, the Overlords, who have HP approaching that of a Behemoth and wield BFG's such as Tri-Beam Laser Rifles and Gatling Lasers. For the hostile humans, there's the Enclave soldiers, who wear Powered Armor and often wield heavy weapons such as lasers or plasma rifles. Broken Steel also has Hellfire soldiers, with fire-resistant armor and Heavy Incinerators.
In Fallout: New Vegas, the major factions have their elite mooks as well. The NCR has Veteran Rangers, who use high-end firearms like the anti-material rifle and are heavily armored, and the Heavy Troopers, who use big guns such as miniguns and stripped-down versions of Brotherhood of Steel armor. Caesar's Legion meanwhile has the Centurions, who command other forces of the Legion in battle and are equipped with the best weapons that the Legion can provide and the Praetorian guard, who use high-end unarmored-class weapons.
The Elite Guards in Mark Of The Ninja. They can't be stealth-killed, are good hand to hand fighters and constantly boast about their martial arts prowess.
The all-red Mooks in the Boktai series that will randomly replace an enemy in a level sometimes. They move around like a bat out of hell, can kill you in only a couple of hits, have tons of HPs, and are better off avoided since you get no rewards whatsoever for actually killing them.
The Madness Combat series features the Agents, starting in the fourth one, where he manages to stall the protagonist...for a few extra seconds. He gets his revenge, however, later in the episode, when he's resurrected as a zombie, and manages to shoot the protagonist. In the fifth through seventh ones, however, they become as common place as regular mooks, until another elite group takes their place as as Elite Mooks. The three appear in the sixth and are quickly killed, and in the seventh, they're highly commonplace.
Likewise, the Bunnykill series features two ninja rabbits as Elite Mooks in the first installment (and are actually challenging), bunny 'agents' in the second (the first two are challenging, but then about ten are cut down easily in a display of Katanas Are Just Better), and the dark-grey (mercenary) and brown (techie) rabbits in the third installment (the techs provided extra challenge, the mercs not so much).
Red vs. Blue features, in the ninth season, Sharkface, a flamethrower-wielding soldier who manages to give a couple of the top Freelancers a tough fight. Lampshaded by Wash when he first appears: "What the fuck is with this guy?"
Later in the same mission, a few jetpack-equipped soldiers prove a challenge.
In The Gamer's Alliance, the Blessed are the Master's most fearsome Totenkopf minions who have the authority to command lower-ranked Totenkopfs. The Coalition's S-Class Mullencamp are an even deadlier group of regular Mullencamp who are efficient warriors and mages surpassed only by the Vulfsatz in effectiveness. Demons of Hoch class, particularly the Black Death squad, are surpassed only by the Dreadlords and the archdemons in raw power and cunning.
One of them shows up as a member of the "Rough Rhinos" that reappears a few times in the series. He might be a subversion since he was actually booted out of the Yu-Yan for failing a critical mission.
The General from "The Blue Spirit" implies that the Yu Yan archers are used only for certain tasks.
The Equalists from The Legend of Korra appear to consist purely of these, though a few trainees and hangers on have gone down easily enough every single uniformed member of the group has been able to give the main characters a good fight. In their first appearance they actually beat the heroes in even odds!
Star Wars: The Clone Wars introduced the BX-series Commando Droids, the Elite Mook version of the standard Battle Droids. They had enhanced armor, nearly General Grevious-level agility, and a number of neat tricks such as magnetized feet to resist Force pushes. They were a decent threat to clones, but still no match for the Jedi (although they were at least able to put up some resistance).
The Monarch briefly employed Black Guards, who appear much more menacing than his regular henchmen (but Subverted as the Black Guards all used to be regular henchmen. Even typical non-action villainess Dr. Girlfriend handles several in a fight without issue,) as seen in the page image, on The Venture Bros..
Also the "Strangers", the team of soldiers used by the Guild, all appear to be Elite Mooks. Brock even seemed to be wary of them the first time they were shown. They have been seen freezing a room of people solid and then administering memory wipes in the event that somebody is about to give away a crucial piece of information.
G.I. Joe: Cobra Commander has his Crimson Guard, who were supposed to be of significantly higher quality than Cobra's basic blue-shirt mooks, but who (at least in the 80's cartoon version) generally proved as ineffective against G.I. Joe's named character squads as the lesser mooks.
At least one or two Crimson Guardsmen got a minor Crowning Moment of Awesome (i.e. the one who fights his way out of a top secret lab in one episode), but would usually screw it up at the last moment with a cringeworthy mistake (the aforementioned Crimson Guard accidentally dropped the chemical he was stealing, creating a giant amoeba that ate him and half the county he was in...Cobra's experiments had a funny way of unexpectedly doing wacky stuff like that.)
The toyline also had the Crimson Guard Immortals, the elite of the Crimson Guard. Possibly a Shoutout to the Persian Immortals
Regular Neosapien mooks in Exo Squad were gradually reinforced with more powerful Neo Warriors and Neo Lords in the second season. Not that any of them had a real chance to harm a recurring character...
In Teenage Mutant Ninja Turtles (2003), the Foot Clan has Elite Foot Ninjas (the guys in the red robes and coolie hats). Unlike many Elite Mooks, these guys actually were demonstrably better than the standard cannon fodder Mooks, able to fight evenly against the turtles and almost killing them in their first appearance.
A big contributor to the Foot Elite always posing a threat would be that there's only four of them.
During one episode of Kim PossibleDr. Drakken discovers how worthless his Mooks are so he sends Shego to steal strength enhancing rings that transforms the wearer into peak condition. They didn't become any better so they were defeated quite easily by Kim (and still proved to be much more reliable than the Elite Mooks by herself...)
The Fourth Mask shadowkhan from Jackie Chan Adventures could be considered Elite, as they nearly had super-strength and were almost impossible to beat without the strength talisman, or similar.
After realizing that his regular mooks just weren't cutting it, Teen Titans Season Three Big Bad, Brother Blood, replaced them with completely mechanical copies of Titans member Cyborg. The Titans still managed to take them down, but it took a lot of strategizing and improvising where ordinary mooks would have just been effortlessly blasted through.
Season 3 of Generator Rex features the "Black Pawns," elite soldiers brought in by Black Knight after she takes over Providence. They wear all-black versions of the standard Providence uniform, and are far more skilled at hand-to-hand combat than regular mooks, even giving Six a run for his money. Later episodes imply that they're now the field commanders for Providence operations, even getting their own custom vehicles.
And even then, when they're at larger numbers, they're usually in their more vulnerable beetle-like forms (which canonically have lighter armour). Insecticoms in this series are subject to Conservation of Ninjutsu, but not to the same jarring degree as most mook squads. When they're at their most dangerous, they tend to fight in smaller squads and provide relatively tough opposition to the Autobots.