Ishtar from the Final Chapter of Live A Live can be described as a random encounter miniboss.
Live A Live also has one in the Prehistoric Chapter and one in the Bakematsu Chapter. They warn you by using the boss music when you encounter them, though- and there's a rather small chance that you'd run into them without knowing.
Kyokushin No. 1 in the Near Future chapter. For starters, they always appear in groups of three, and they use several powerful attacks, such as Wheelie Kick and Cow Killer, the latter of which can (and will) one-shot you. Oh, and they have high HP, defense, and evasion! Have fun.
Abyss Bat in SaGa Frontier; granted that you have to wait around for him to show up, but he puts up quite a fight.
The Leprechauns in the second game's Holst Mine have 2500 HP when every other non-boss enemy until then has had maybe 200, tops, and your party members are probably still barely breaking triple digits in damage without spamming ARM attacks or exploiting elemental weaknesses.
The Amazee Dayzee in both Paper Mario and Paper Mario: The Thousand-Year Door wholly crosses over with Metal Slime. It might just look like a sparkling Crazee Dayzee, but it has 20 HP (most of any mook in the first game, and tied for second-most in the second game, behind the Dark Koopatrol), 20 Attack, 1 Defense (in a game where any sort of defense score is notable), and their attack can also cause sleep. It also has an attack that has unintuitive timing to defend against, and definitely needs a lot of strategy to beat...because, due to its Metal Slime nature, it's likely to run away first chance it gets. Especially in The Thousand-Year Door, where if you actually encounter one on the map (completely by chance) the first time you go through that area, 20 damage will be almost enough to kill you from full HP. And then on the return trip from said first journey you have no partners, and have to pray that it will run. More than capable of murdering any unsuspecting player.
Thousand Year Door provides a decent way to beat them once you get the Ruby Star and gain Art Attack. By concentrating loops around the Amazee Daisy, you can hit it for enough Armor-Piercing Attack damage to beat it (or at least leave it just one good hit away).
A lone Elite Wizzerd in The Thousand-Year Door probably isn't tough enough to count (despite having both the "needs a lot of strategy to defeat", to some degree, and the "has a variety of different attacks" qualifications). Unfortunately, they generally come in groups offour or five. A defense of 5 is almost insurmountable in this game, so you pretty much need to use defense-ignoring attacks (here's hoping you've got plenty of Star Power—Art Attack works well, but even from a full meter, you can only chain two of these). They have 12 HP each and have three different damaging attacks, one of which does 8 damage to one party member and one of which does 7 damage to both party members. They can also buff their attack or defense, become dodgy (attacks may miss), become transparent (attacks will miss), electrify themselves (deal damage if you try to attack them directly), heal themselves, and when only one remains, it will inevitably split into five, only one of which will actually take damage. And they only appear on the lowest levels of the Pit of 100 Trials, after you've likely worn out your items and star power fighting Piranha Plants and Dark Bristles on the previous stage and regular Wizzerds on the stage before that.
Amayzee Dayzees: They have lots of HP in both games, and have lots of Attack power. They can also run away a lot quicker than Bandits.
Super Paper Mario features an enemy called Mega Muth, a white mammoth like creature found in Castle Bleck. Numerically stronger than the final boss, you have to fight a whole corridor full of these things. In fact, Tippi outright compares them to gods. Luckily, they're slow and can easily be dealt with by throwing them at each other. But there's an even stronger subspecies in Flopside's Pit of 100 Trials...
Paper Mario: Sticker Star has a Toad who gets beaten up once in each world. While most fights involving him are special, long time fans should be suspicious when a duo of Shy Guys are beating him up. Rest assured, they are a Call Back to Anti Guy and give themselves a massive stat boost when the fight starts, being one of the few, if not only, regular enemy fights to exceed 100 HP.
The Archmage and the Berserker, enemies in the Container Yard of Breath of Fire III are actually tougher than the final boss. The Archmage even has a skill that revives your entire party. Why? So he can kill you again.
Similarly, the Rider enemy in Breath of Fire IV is much stronger than the final boss, using the game's strongest spells on the party, and healing itself an absurd amount every turn.
Breath of Fire II already contributed the K. Sludge and the N. Rider to this trope. The former came in groups of three and packed a very effective Instant Death spell, and the latter can use all of the highest level spells in the game.
Suikoden occasionally likes to toss high-level monsters onto the overworld map just to mix things up. This is usually accompanied by a change in battle music.
Dungeon Siege has this to some degree: occasionally you'll see enemies lit by a Pillar of Light, with the same attack power but usually 3 times more HP than your average foe. The third game does away with the pretense and gives them the same onscreen health meters as normal bosses.
Etrian Odyssey, being a Nintendo Hard dungeon crawler, has a ton of these monsters, designated as "FOEs" (shorthand for Fucking Overpowered Enemies) in game terms. First appearing on the second level, they appear as arrows on your map, and most of them look exactly like the normal enemies in the dungeon...but have vastly higher HP and attack power. Some follow set movement patterns, while others will rush your party when you get in their line of sight. Others, once they sense blood (such as the Wolves and Skolls) will actually join other FOEs mid-fight to make your life even more of a living hell.
The sequel, Heroes of Lagaard, in addition to having a F.O.E on the first floor, takes this one step further. A specific random encounter has 10,000 hit points, more than five times the number of hit points of the next strongest random encounter, and 3000 more than the strongest FOE the game has to offer. Said random encounter also has a multihit attack on your entire party what will usually OHKO any of the non-tank classes, as well as a skill that prevents you from using any of YOUR skills. Said random encounter also holds the dubious distinction of being the only FOE or random encounter in the game that is immune to Instadeath Skills (most Bosses are immune), and the ONLY enemy in the ENTIRE game that is immune to Stun. 'Boss in Mook Clothing', indeed.
Dragon Zombies and their Palette Swaps have huge amounts of HP and nigh-impenetrable defenses. Most of the time, the only way to defeat them is by equipping the Dragon Slayer weapons.
The Palette Swaps of the Hel Servant boss, the "Eye" monsters hit hard, possess a nasty array of spells and attacks and will revive each other to full HP if encountered in groups of two or more and if they're not killed in the same turn. Thankfully, there are only one to two "Eye" encounters in most dungeons.
Right before the final Bonus Boss of the Seraphic Gate, one of the encounters is usually a Loki Shade, a Palette Swap of an end game boss. Tough, but doable. However, there is a small chance that you will fight Hamsters instead. Normal looking, regular sized hamsters. Their small size means most attacks will simply whiff over their heads, and they possess an array of devastatingly powerful spells and attacks, including Furry One, which unleashes a stampede of hamsters on your hapless party For Massive Damage. Prepare to die.
The elephants in The World Ends with You. They spam an annoying attack - a stomp creating a slowly widening shockwave - that can interrupt any attack. Easy enough for Neku to dodge, but you might have to actually start paying attention to the top screen so your partner doesn't end up making you die. Even if you're using the partner that can float in mid-air! The damn ground stomp knocks him out of the air!
Also, the final two Pigs, Pig Butoh and Pig Mazurka, are the toughest Pigs by far. The former is the only Pig who actually attacks you, and is quite powerful. Beating him unlocks Pig Mazurka, the king of the Pigs. He's a Flunky Metal Slime who uses the Frogs he attacks you with to get away. Oh, and for both fights, you're limited to Gatito and Unbranded pins only. Oh, and your reward for beating them besides unique pins? The chance to fight Panthera Cantus himself.
Hell, it's practically a given that the random mooks in the last (and possibly next-to-last) dungeon in all Megaten games will all, without exception, be totally immune to every kind of attack save one. Don't have that damage type/status effect in your group? Why, I believe it sucks to be you right now. Have it, but the character is out of mana after running into one of them too many? Oh, but your tears of frustration are just yummy, my dear.
An egregious example would be the rainbow-colored Maya in The Answer (Persona 3). It has high resistance to damn near everything except Almighty attacks plus can nuke pretty much any party member with Black Viper (single target Almighty spell). Woe unto you if it hits Aigis.
The Avenger Knight, also from The Answer, will teach you not to mess with the tiny, red Shadows. Insanely high HP, blocks light and bounces back dark, reflects Aigis' physical attacks, and has no weakness. It also hits like a truck with strong Zio (electric) and Slash attacks.
Jotuns come with ridiculously high defense. Even if you're exploiting weaknesses the whole time, it'll take a while to kill one. Naturally, when you finally encounter one as a boss, it absorbs all damage except for one type.
Persona 4 sometimes features random encounters ten levels above the norm for the particular dungeon they may be found in. These enemies will generally be able to kill anyone in your party in a single hit - and sometimes all of them in a single attack. Even then, there are encounters in which you'll be up against three or more enemies your own level who all cast high-probability instant party kill spells every turn. Also, despite the fact that it's relatively forgiving for an Atlus game, if the AI lines up just right then a normal encounter you've blown through 20 of in that dungeon will suddenly become frighteningly competent and cause a near total party wipe, even on easy.
There is a particularly annoying team in Devil Survivor. The Leader: Some Magic-prominent reviver/healer. The other two? Berserkers. Who always have Endure as their one of their abilities, which allows them to always survive an attack with 1 HP left. Needless to say, it's almost impossible to take down even one Berserker AND kill said leader before one is revived, and the leader gains almost perfect defense again.
There's also the Decarabia. Offensively, they're decently strong with their fire spells, but nothing special. Defensively, on the other hand...they have Shield All which they abuse often, and have Sacrifice, giving them health at the end of every turn. Pair them up with two strong fighters, like Berserkers (mentioned above), and you have a group of monsters that are difficult to hit, deal high damage, and will end the fight with full health.
There is a complete reversal of this is in Digital Devil Saga. The final secret boss is the Demi-fiend from Nocturne. His random encounter music plays during the battle, giving the impression that you're just a random bunch of mooks for him. And quite frankly, if you're not prepared, you are.
For a more straight example, there's Samael in the Karma Temple and Anahata Waterways. A Samael in this game has more than a thousand HP, 666 MP, resists Physical, voids Earth, repels Electricity, Expel and Death, and has some nasty skills like Vanity and Revelation. Two of them can appear as reinforcements if you defeat an enemy encounter in the waterways, but Samael is typically alone.
Shin Megami Tensei: Strange Journey has a system of special battles in which you use a special visor to find rare demons and battle them. Most of the encounters found this way are quite strong, but drop valuable remains which can either be sold for a lot of money or used in high-end weaponry. However, every now and then, horrifically overpowered demons pop up. The finest examples are the Fiends, but there are plenty of others who occasionally come up with a hankering for your guts.
One very-often-deadly example: You're level 17, you just got the Enemy Search app, and you're happily wandering around Sector Bootes to test it out. Oh, hey, there's one! An unknown, but that storyline Enemy Search was just a Fomorian, so it probably won't be too ba- *level 27 Kishin one-shots the hero with Zan-Ei*
Shin Megami Tensei IV also has the Fiends appearing as possible random encounters. However they are only found in a few locations, are exceedingly rare, and when one is around Burroughs warns you. So it's more of an example where you will have to deliberately be searching for them to most likely find one.
Persona Q has large shadows in each dungeon, which have much more HP than any other shadow and can act twice per turn (although they have a chance to waste an action).
Wizardry VI: Bane of the Cosmic Forge, from a series known for random encounters sometimes being tougher than bosses, has a very, very low chance of the party encountering a Tyrannosaurus Rex in the final outdoor area of the game. It's unlikely you'll see one in six or seven games, but if you are that unlucky, it is game over. Nobody has ever successfully taken down a Tyrannosaur.
Mother 3 - One word: Cattlesnake. It has more than twice as much HP as any other enemy in the area (it has almost 800 HP, and the nearest enemy in the area in terms of maximum HP only has around 250 HP), and has a ridiculously high defense - characters that do 50 damage to other enemies will only do 10 damage to the Cattlesnake. It also has an attack that can hit the whole party for 70-80 HP damage per strike - at a time when your characters will average about 140 HP. Before you first see one, there is a sign warning you to keep your distance.
Cattlesnakes are a threat in Chapter 4, when you have only two underleveled characters, but by Chapter 5, your now-fully-assembled party can eat it for breakfast. There's no reason to, however, because their experience yield is as much as other, easier to defeat enemies in the area, or at least don't yield enough experience after dying.
On the subject of EarthBound: Final Starman in the final dungeon. Capable of spammingPSI Starstorm Omega, which deals over 700 HP of damage to the opposing party (and only Ness even has that much HP when you encounter it); Brainshock Omega, which confuses everyone in the party; and Healing Omega, which fully revives any defeated enemy. Oh, and they start out with maximum PSI shields, which completely deflect PSI attacks. Couple that with the fact that they usually appear with Ghosts of Starmen (see Demonic Spiders) and Nuclear Reactor Robots (spends its turns healing enemies to full health AND explode when you kill them)...can you say Total Party Kill?
The volcano enemies in Fire Mountain before Saturn Valley in Mother 3 are also this. Entering the dungeon means that you face enemies that chop off half of your HP with each shot, at your entire party. And please don't get started on New Fassad...if he doesn't murder you, the enemies will.
The Nintendo Hard RPG The 7th Saga has a variant: every random encounter is like this. The bosses themselves are often significantly less likely to kill you than the random encounters in the dungeon that contains the boss.
The Sootie family in Star Ocean Till The End Of Time's Bonus Dungeon Sphere 211. A single one can easily kill a level 255 party (which is downright absurd, considering the fact that the game's uber-Bonus BossFreya can't even damage characters that the normal enemy Sootie Sister could kill in one or two blows), and they are a pain in the ass to even hit. Demonic Spiders much?
Star Ocean 2: The Second Story has this pretty much at many points of the game. In many dungeons there will be enemies that will instantly petrify your party, and will require constant stunning to prevent the group-petrifying attack. Attacking so often the enemy can't do anything is a major tactic for most enemies. In the bonus dungeon, most of your characters will have a Star Guard, equipment that upon a successful block, will do an attack which releases multiple attacks that can do 9999 damage a piece, and even then, you will die if not careful.
The Might and Magic series had this whenever you face a spellcaster. If it could cast certain spells, you were simply doomed. Namely, Meteor Shower (with which you could often kill your OWN PARTY with) and Shrapnel are two of the most deadly, and sometimes Death Blossom could also put you in a world of hurt.
Don't forget Finger of Death which was a one hit kill, or Eradicate which literally destroyed one of your parties bodies so that they could not be brought back to life with the Raise Dead skill. You needed an even more powerful Resurrection spell to heal them.
Phantasy Star II had Blasters in the Bio Lab and Nido Tower areas. If you met one, your best bet was to either run or nuke it with every single bit of firepower you had. Meet two? Pray you can run, OR ELSE.
In Phantasy Star IV, the first Sand Worm you fight (usually) is a boss. However, when you get your first vehicle and cross the sand pits, you'll encounter them as regular mooks. That first sandworm is that it's an extremely difficult boss fight when you first get to where you can take the mission for it, often capable of killing or at least severely wounding a party member per round, before you have access to resurrection items— and that one doesn't have all the regular Sand Worm attacks. It can't use Earthquake, which will destroy an un-buffed party even twenty levels later. The kicker is that one of the types of little worms you fight in Motavia will run off and summon another full-powered Sandworm if you even leave one of them alive. Surprisingly though, Sandworms do provide a hefty amount of Experience points, despite their difficulty, if you pull off the right combinations you can just set a Macro based off of that turn to toast it every time.
It's a good thing Avernum 5 only does a mild version of this, because it gets used constantly.
The Game Boy RPG Robopon has - erm, well, quite a lot of them. Perhaps the worst offenders, though, are Move-typeRobopon. They use attacks that increase their speed to insane levels, making it almost impossible to land hits on them. To make matters worse, they generally have either high Attack or Defense, meaning they'll either pulverize your team into the ground in seconds or take what hits you do land on them and shrug it off like it's nothing. To make matters more insulting, when youuse Move-types, they often end up gimped because The Computer Is a Cheating Bastard and has access to better moves and equipment than you do.
Some of the enemy monsters in Monster Rancher have a tendency to be much more powerful than other monsters, even of their rank—and it's not just the ones intended to be stronger, like those used for invitation matches. Enemy Gaboos in Monster Rancher 2 tend to have ridiculously powerful moves, as do Golems—in any game.
Fallout 3: Deathclaws are exceedingly ferocious and can demolish even high-level players if they are caught unawares. Super Mutant Behemoths are considered the "bosses" of the game, as there is an achievement for killing them all, but players have proven that a Deathclaw can kill one in 1v1 combat.
While not quite as lethal, the Mirelurk Hunters and Giant Radscorpions deserve honorable mention. They are much stronger than their weaker variants, come out of nowehere once you hit a certain level, will kill you if you haven't been upgrading your combat skills, and the Mirelurks take very little damage unless you Attack Its Weak Point.
Those are all actually extremely easy with the proper use of landmines, which you should have by the time you encounter them.
Also with an easy-to-get and easy-to-get-early Lincoln's Repeater with some Sm Guns skill and VATS-aiming at the face.
The Yao-Guai, when first encountered, can be like this due to its ludicrous speed and raw, unstoppable power. Your only hope before you can easily kill them through over-leveling is to catch them as far from you as you can and shoot them in the head as many times as possible before they close the gap between you and them. Due to being able to run into them before finding the shotgun, they can be horribly brutal, nearly impossible to kite, and sometimes come in pairs. They're also quite capable of taking a full mini-gun burst if you aren't skilled enough. Yao Guai and Deathclaws are the single biggest reasons to find and craft a Dart Gun as quickly as possible. The weapon cripples the legs of anything it hits, and a Yao Guai or Deathclaw with crippled limbs, in addition to being a great deal slower, also cannot lunge.
Fallout: New Vegas dropped the Dart Gun and made the Deathclaws more numerous and resilient, turning them into outright Demonic Spiders. Fortunately, they only appear in specific locations as opposed to random encounters.
Sentry Bots have the same HP as Deathclaws, with even greater damage resistance and no weak points, and possess highly damaging weaponry in the form of a Minigun or Gatling Laser and Missile Launcher. They also largely replace the lower-grade robots at high levels. Once you're leveled up and have the proper weaponry, though, they become more of Fake Ultimate Mooks.
The Broken Steel expansion DLC adds Super Mutant Overlords, Feral Ghoul Reavers, and Albino Radscorpions. All 3 enemies have incredibly high boss-level health and massively damaging attacks. Even high level characters can find that an entire VATS cycle of high-end attacks that can kill all other enemies in just a few hits will barely scratch their health meter. They can appear in any location where their lesser brethren spawn, even if you had been there at a lower level. As early as Level 13, in fact.
The Overlords and Albino Radscorpions are at least used like bosses, in that you rarely fight more than 1 than a time (2 or maybe 3 at once in certain very specific situations, including Vault 87 if you're above Level 20, and GNR Building Plaza at Level 15+). However, there are multiple free-roam dungeons(e.g. Red Racer Factory, Franklin Metro Utility, and Dunwich Building at high levels) and one main plotline mission (Presidential Metro) near the end of the game where you're expected to fight several Feral Ghoul Reavers at the same time. Bear in mind each individual Reaver is about 1/2th as tough as a Behemoth, and hits almost as hard.
Worse, there are certain places where these enemies can spawn regardless of player level, for example, you can encounter an Overlord outside GNR as early as Level 6. And God help you if you run into a Reaver in the Metro tunnels at that level.
Speaking of DLCs, Point Lookout had the Swampfolk. They look like normal (if slightly deformed and deranged) people, yet their attacks hit for much more than you would suspect. This is because they, like Deathclaws, have the ability to ignore your damage resistance. But unlike Deathclaws, they do not have sharp claws or other special abilities. The developers have said that they made the Swampfolk so strong because they wanted Point Lookout to be the hardest DLC and also because they wanted to create the "Lovecraftian" feeling of having to run and hide from mysterious enemies; instead of just running in and slaughter everyone with your minigun. The aforementioned Reavers are also a common occurence. Swamplurks look like a palette swap of the base game's Mirelurk Kings, but have almost twice the HP, twice the melee damage, and spit armor-eating acid that does as much damage as a Deathclaw.
The original Fallout had a single Deathclaw as an incredibly rare random encounter while traveling on the over world map; considering most of these random encounters are generally more of an annoyance than a challenge after awhile, any person playing Fallout for the first time was in for a slaughtering.
In Fallout: New Vegas, the game introduces a new enemy type known as the Cazador, which although very small and having the appearance of a much weaker enemy, the Bloatfly, can decimate low level players with its poison within a couple of hits and as nimble. Not to mention, they come in packs of up to five. They are often used to wall the low level player in, forcing them to take a specific route in order to level up first.
Infamy with the Legion, which is likely to happen early on, will cause them to send Assassin squads after you that are much tougher than standard Legion mooks, even the less armored ones, and at higher levels they wear Centurion armor (with higher Damage Threshold than the Final Boss) and carry DT-ignoring chainsaws, super sledges, thermic lances (which also ignore armor), marksman carbines, and anti-materiel rifles.
Old World Blues' Robo Scorpions attack in large groups, scale to your level, can take more punishment than a tank, and are armed with very damaging stinger lasers.
The Courier's Mile area in Lonesome Road has Irradiated Marked Men, who have more HP than Deathclaws, and since they're ghouls, the high radiation in the area regenerates their HP, faster than the normal Marked Men. They are also heavily armed and come in groups.
On the subject of Deathclaws, the Alpha Male and Matriarch variants are twice as fast as and have 50% more HP than the vanilla version, and deal up to 300 melee damage (Normal difficulty), which means a One-Hit Kill to most characters. The Lonesome Road Deathclaws, since they scale to the player's level like most DLC enemies, become even more lethal than the Alpha Males at high levels, able to One-Hit Kill nearly any character.
At the end of Veronica's companion quest, depending on your skills and dialogue choices, you may have to fight a group of rogue Brotherhood Paladins, who are decked out in the almighty T-51b power armor and wield some of the game's most powerful weapons, including the potentially One-Hit Kill Gauss Rifle. Their stats also scale to the player's level.
These are so common in Mana Khemia: Alchemists of Al-Revis that they actually get their own battle theme and a special icon in the game's Preexisting Encounters system. Early examples include the Bear, Owl Bear, Sword Geist and Shield Geist. You also get twice the normal AP for winning a battle containing one or more of them, so they can be worth the risk. Yes, the game gives this much fanfare to regular enemies that are much harder than the norm. Appropriately, actual bosses, by comparison, have a downright epic battle theme and look about as intimidating on the map as a red blob can.
A series of random enemies in the bonus dungeon take this Up to Eleven, being tougher than any Bonus Boss in the game. They have levels of health normally reserved for bosses, more than enough power to KO your team, tend to gang up, and are much faster than regular enemies on the field map, so good luck running past. To top it all off, only a critical hit can deal significant damage to them. And by "significant," we mean "more than one point". Fortunately, there are waysto compensate.
In Wizardry V, there is an optional level. If you go down there, the enemy strength widely varies. You might get some ghosts, which do almost no damage and have very low HP...or you might get enemies like Dark Lords and Arch Fiends who have several times more HP than even the end game boss and spam the best magic in the game, including a spell that can kill your entire party at once if you're unlucky and another spell that does around 100 damage to everyone when triple digit HP is a big deal and healing is hard. They might attack you normally instead, in which case the target, if not killed by raw damage is probably instant killed anyways, and drained about 5 levels. They also spawn with lesser (but still powerful) demons, who throw in more firepower. Worst part is while you aren't technically required to go down there, it's the only way to get the best equipment in the game, which among other things gives you the magic resistance you need to not die in 1-2 rounds against...nearly any late game enemy. Especially the aforementioned end game boss. To be fair though, it does play the boss music to warn you...but it's still a random encounter, and you might not be able to escape.
Slivers in Tales of Symphonia, a slightly less powerful version of the Sand Worm (also technically not a boss, but not encountered randomly and guarding one of the Devil Arms). They appear very rarely in the snow fields near Flanoir. Very, very rarely. Will probably be the last monster you need to complete your Monster Guide.
The second (optional) Card Key in the Iselia Human Ranch in the sequel is guarded by a group of tiny leeches...with ridiculous amounts of HP that they constantly heal, and that deal a ton of damage. If you don't have very strong mons with you, you are certain to get party wiped unless you use the run command. If you do have very strong mons with you, you are almost certain to get party wiped.
The Bahamutt enemy in Super Mario RPG straddles the line between this and Sub Boss, as it is only encountered when summoned by Chester or Magikoopa (a Chest Monster and Boss, respectively). It has a unique sprite, packs stats that are stronger than most bosses fought in the final area and is one of two non-boss enemies to have over 1000 HP. Finally, it has an attack that causes Fear, which halves a character's Attack and Defense.
A Chest Monster named Box Boy resides in Bean Valley. It packs really high HP, Attack and Defense at the point in the game you face it, a strong single-target magic attack knows as Blast, an attack that causes Fear, and an insanely powerful Carni-Kiss attack that can deal around 90 HP more damage than your characters have. It's also immune to fire, ice, and thunder magic. Alone, it's a force to be reckoned with, but it also has the need to summon a Fautso in every battle, which also has an immunity to fire and thunder (but not ice) and can use Boulder, a powerful non-elemental magic attack that hits the entire party; and Aurora Flash, which puts your entire party to sleep. Have fun with this boy.
To be honest, ALL FOUR CHEST MONSTERS can be considered this, though there's only one of the other three types... but they respawn if you leave the area. There's Pandorite in the Kero Sewers, Hidon in the Sunken Ship, and Chester in Bowser's Keep in addition to Box Boy. All of them except for Pandorite also spawn special enemies that are rather tough. Luckily, the Chests are weak to one element. It's Jump, of course.
Dactyls in Titan Quest only look a little different than other mooks in the dungeon where you find them, but they will paint the floor with your innards if you aren't expecting anything different. Then they'll do it again if you were expecting something different.
In Eternal Ring there is a secret area that is reached by going back through the starting cave and hitting the door on the beach with a dark or light spell. Inside are rats that are easily one-shotted, floaty orbs that die in three pokes of a sword, but go on a (long) self destruct timer, and the werewolves. They take several castings dragon summoning spells (dragon spells are as big as it gets here), and they take more than half the HP of a character who's already able to take on the final boss.
The Black Rabbite of Seiken Densetsu 3 is just a palette swap of the conventional Rabbite. It's also the most deadly thing in the entire game.
Mega Man Battle Network 3 has an entire series of these in the form of the Omega Viruses. Every type of enemy in the game has a fourth level of virus that is super-fast, super-powerful, and pack high HP (some Omega Viruses get up to 500 HP, about the same as an early-game boss). Some will even have additional effects added to their attacks (e.g., Mettaur Omega's shockwave now cracks panels). Thankfully, they're only found in set encounters late in the game.
There's also the Scuttlest. Normally, the Scuttles are Demonic Spiders, even being a spider. Their traits are elemental gimmicky attacks and an aura that needs to have 100 damage done in ONE GO before they can get damaged. Enter the Scuttlest, which usually comes with the Scuttles, and might even come along with the Scuttle Omega which is even worse. It has an insanely powerful beam attack that goes through and might BREAK every obstacle, has hp from 200 to 400, their aura takes 200 damage in one go to destroy (a trait only shared by the proper Bonus Boss, Bass), the aura can come back AND their attack deals 200 damage (300 for Scuttle Omega), which is lethal as far as Viruses go and hard to dodge as the laser takes a whole row and you're likely dealing with the other Scuttle's attacks, and it also means if you have the Life Aura, which puts you on common ground with them, it'll go away instantly with a single attack, so you have to actively dodge them even with the Game Breaker defense chip.
In Mega Man Legends, you can run into a Boss in Mook Clothing while exploring the tunnels connected to the subgates. After going through a bunch of rooms with nothing but Death Traps, you enter a room. Immediately, there is a crashing noise that's almost louder then the 'Bee-Boop' warning sound. After you run for your life, you get to a big room to see an upgraded version of the very first boss in the game. However, there's a big difference - the first boss had one drill; this thing has TWO. Due to the somewhat cramped quarters, its smash attacks are difficult to dodge, and they take a good chunk of your life bar away. Not only that, but it also can fire both drills at you all the way across the one large room if you get too far away, and it takes a ton of punishment before croaking! Thankfully, this is a unique Reaverbot only found in that one area.
The Cyclops enemies in Sword of Mana. They each have a 5% spawn rate in a single area on the correct day of the week. They are huge compared to most normal enemies, possess an enormous amount of HP, have very high stats, and will richly reward you with their high drop rate on aerolites. They're also a great source for leveling up weapon and magic skills.
Kingdom Hearts 358/2 Days introduces a couple of these. Invisibles have had a major upgrade from the first game, but the game warns you ("Caution! A powerful enemy is near!") so they may not count. Living Pods, on the other hand...Crazy amounts of HP and they hit like a semi truck. What looks like an easy mission becomes a pain in the ass thanks to these guys.
The Black Fungi from the first game count. They have low HP, but absurdly high defense, they don't flinch at your attacks, they release poisonous gas which will do pretty sizable damage to your party, and they spend about half the time encased in stone so you can't even hurt them.
re:Coded has the Eliminator, a recolored Defender that randomly appears in System Sectors. They can block any frontal attack or magic? Not too bad, normal Defenders can also do that. They can also teleport around the sector, and have crazy attack power. What makes them truly evil is their shield attack, which fires a fast-moving homing burst that can inflict any of the status ailments in the game. Better hope that it is not flip-foot or Level 1 Defense...
At least Invisibles and Black Fungi let you beat a hasty retreat if you so wish. Eliminators, on the other hand, willTeleport Spam to stay within attacking distance of you. If you're fast and lucky enough, you may be able to reach a door before you get killed.... only to find out that the blasted things actually follow you from room to room, something that no other enemy in the game is capable of doing.
Harbinger, in Mass Effect 2, would be a literal example, but is not actually that particularly difficult. He randomly assumes direct control of Collectors, making them a lot more stronger and durable than normal and adds the ability to launch explosive projectiles that can hit you even behind cover. And even if you kill him, he'll just find another body if any are still present. Usually you have to kill him three or four times in a single fight with Collectors. In basically every fight with Collectors.
The Scions can be quite tough nuts to crack as well with their very powerful ranged attack than can disable your shields on a single hit. Made worse by the fact that they usually appear together with big swarms of Husks.
Thresher maws in the first game. They can be defeated quite easily once you have them entirely figured out, but you need to make good use of the rocket launcher and machine gun of your vehicle to take them down and they can destroy it instantly when they erupt right from under it. Two hits from their acid spit also can destroy the Mako.
A Thresher Maw actually appears as a full-fledged boss in Mass Effect 2 in Grunt's loyalty mission.
Mass Effect 3 adds the Banshees, which are probably the prime example of Bosses in Mook Clothing in the entire series. They are presented as rare but regular enemies, but are easily the strongest and most dangerous of all Husk forms. Made from Asari with a rare genetic anomaly, they are not only very tough and durable but also possess extensive biotic abilities which allow them among other things to cover medium dinstances almost instantaneously to pop up right next to you. And did we mention they have an instant-kill melee attack? To make things even worse, they usually appear in groups of two or three. Accompanied by swarms of lower Husks. And then there's their scream.
Mass Effect 1 included the nameless Krogan Commander, who has two lines at best and is not much different than a normal krogan, but just catches the party at the right range to make him a very nasty encounter. He serves as a final boss for the level despite his build as a mook.
Demon's Souls features at least one kind of super-nasty enemy in every world, and most of them have the ability to instantly or near-instantly kill you if you make a single mistake fighting them. Usually the dangerous enemies are Black Phantom variants of existing ones, easily distinguished by their black and red glow. The Boletarian Palace has red-eyed knights who can very easily break through your guard. The Tower of Latria has Mind Flayers, who can blast you from afar with strong magic projectiles, and shoot a paralyzing burst of electricity that lasts just long enough for them to walk up and slaughter you. The Shrine of Storms has four kinds of skeletons- long sword wielders that roll up to you and break your guard with overhead slashes, archers that fire magic arrows, golden-armored skeletons with huge swords, and black-armored ones with dual katanas. The katana skeletons are the meanest by far, since they swing their swords in such wide arcs. If you encounter a Black Phantom katana skeleton and try to block its leaping attack, you'll get to watch both your stamina and your health drop to zero in a heartbeat.
Digimon World Dawn & Dusk feature three Digimon per game, which appear in certain locations after the player beats a lengthy Boss Rush. The weakest of them is strong enough to wipe the floor with the strongest opponents from the boss rush. They also are extremely fast, so if you happen to run into two or three of those in one battle while unprepared, it is almost guaranteed that you'll see your whole party fall without even assigning a command.
This happened in the SegaCD game Vay near the end, since Working Designs "adjusted" the difficulty to the point where killing a dragon enemy was boss level difficulty and yet would when killed only give the experience of a weak enemy.
In Morrowind, Ascended Sleepers can be this, being nasty high-health spellslingers that pile tons of damaging effects on you. Fortunately, they're very rare, only appearing naturally once you're over level 20 (they also appear, completely unchanged, as named bosses).
Ditto Skyrim and its Dragons, with the exception that their appearance as random encounters is triggered by the plot rather than by character level.
High-level draugrs(overlord and deathlord flavors) are definitely this. Once you reach a high-enough level, these draugr which previously served as an area's boss now becomes a mook, and they're still every bit as tough as they were before.
The Highwayman from Chrono Cross, which at first just seems to be a scripted encounter. Then you find out it's got a mountain of health, sizeable defense, and an attack that blinds the whole party.
The Beebas as well, when you first fight them.
The flash game Epic Battle Fantasy 3 has the Monolith enemy class, which is nigh-unanimously considered ridiculous by any reasonable standard. All three of them have a ton of HP, resist virtually everything, have incredibly overpowered attacks in general, and have a move that is That One Attack by that standard. The first one you encounter is the Viking Monolith, whose That One Attack hits the entire party, can kill in a minimum of three hits, and inflicts the dangerous freeze condition at an obnoxiously high rate. Oh, and it can cause instant death with another attack. The second is the Ancient Monolith, which loves to pull out a move that heals 100% of the HP of the entire enemy party, including itself, right when you're on the verge of finally killing the damn thing. And then...there's the Cosmic Monolith. It can, and will, abuse its Doomsday attack that nails the whole field for upwards of 10,000 damage. This includes itself; by the way, it absorbs the attack element. And they have a random chance of spawning during the final battle. Have fun.
Do not forget their buffing spells. In a game where Useless Useful Spell is largely averted, an enemy that possesses a max-level buffing spell with the ability to use it on the entire enemy party is a huge Demonic Spider for that reason alone. And the Ancient Monolith can remove your buffs, too. Add all of this to what is mentioned above and...yeah.
Your one saving grace is that they don't null Syphon (instead being just neutral), so if you can pull it off, they can't do anything while you wail on them.
The final area of the game contains a fight with 2 Cosmic Monoliths. Considering their first attack is always programmed to be Doomsday, they're damn hard in any circumstance, even without the limit cap during the first run. Thankfully, all of the encounters in that area before the final boss can be avoided.
Oh, and the final bonus area? The fight there has one of each Monolith type. To add insult to injury, your party's maximum level under normal circumstances is 30. THEY'RE AT LEVEL 50.
Cosmic Monoliths proved so notorious in the third game that the fourth game made them the strongest summon in the entire game, and removed them entirely as enemies...unless you're willing to pay for the DLC level, where you encounter one as a Bonus Boss. Attempting the same tactics that worked on the Cosmic Monoliths from 3 won't work on this one, since it now has a devastating physical attack if it gets Syphoned, and Doomsday now hits through your Dark resistance. And then when you beat it, three more take its place. It even gets battle music entirely unique to this one fight, an honor shared only with the Final Boss!
Both here and in the next game, you'll occasionally run across a Giant Mook that has much more health than its smaller versions and many stronger attacks, and can summon its smaller counterparts too, at will!
The above are less to be feared in Epic Battle Fantasy 4, but there you'll occasionally run across either an already Giant Mook or one or two Demonic Spiders or Goddamned Bats that are slightly larger than normal but several levels higher than the ones around them, and these are a lot harder to see coming. They're usually not guarding anything (and thus will respawn), and many times the enemy displayed on the overworld is a smaller type. And if these are in multiple waves, the big guys will only show their faces on the last wave. And you rarely get much of a reward (aside from experience) out of them.
Anyone who got any ways into the story of Vanguard Bandits will remember the horrors of the Sharking. Each one is nearly a match for your strongest units and they will outnumber you. In-universe, they were designed to kill pilots, and everyone is horrified to see them.
In Cross Edge, Lujit, a teensy pink dragon, straddles the line between this trope, Demonic Spiders and Beef Gate. You can most likely meet in a dungeon where your party is at most level 40. His level? Level 120. WAAAAY higher than THE True Final Boss. To make matters even worse, Lujit has both Parry and Perfect Barrier, which allow it to dodge both physical and magical attacks respectively when its HP hits 25%, meaning that the only way to damage it past that point is EX Skills. Good luck surviving long enough to use those. His attack of choice. A-Fear. Yes, the Big Bad's ultimate attack, and you can die from it this early. And to a little pink dragon no less. Lujit, however, can be easy provided you get him with a group of enemies, since you can kill them to get SP for the EX Skills. If you see him alone, however, run.
So, you're playing Baten Kaitos Origins? And you just got past that damn bird, so you're feeling good? Well, you're gonna saunter away from the crash site and run right into the Alraune. For starters, the flower has a ton of HP, capable of swallowing your strongest attacks for several turns. It's quite fond of 'Poison Breath', which hits all three characters hard and is likely to poison at least two of them. Its normal attacks are no slouch either, and the Mirabilis it comes with hit just as hard. Unless you're loaded for ice or fire, the damn thing can and will rip you apart. Just to add insult to injury, the overworld sprite appears in a very cramped location, making it tricky to dodge. Probably the best way to handle a party with one of these is to assemble Blazing Glacial Queen, but good luck keeping Guillo alive long enough to pull it off.
So, how could that be worse? Well, how about if they made it incredibly common, as in, most enemy encounters will have one. Then, make it appear with several enemies that hit hard, have quite a bit of HP, and have cooperative attacks with the thing. Buff up its stats a bit, make Poison Breath even more painful-wait a second, we just described the Queen Alraune, found all over Nekkar! Have fun!
The Herculean Dragon from Tarazed Core. Its attacks don't hit particularly hard (by this game's standard, at least) but that's small comfort when the damn thing buffs up its defense and heals itself faster than you can damage it, turning a quick battle into a drawn out slugfest. Not even The Apotheosis can kill this thing easily.
The Black Knights in Dark Souls. Non-respawning enemies who appear slightly off the beaten path, they have a lot of health, defense, and are very hard to defend against with fast, powerful attacks.
Titanite Demons, also known as Prowling Demons. They are gigantic (in a game where size is a very good indicator of a monster's strength), there's only a handful of them and they don't respawn, and they are devastatingly powerful. Cruelly, the first one you encounter will be the one beneath the Undead Parish (unless, of course, you find the one in The Catacombs first), who is in a humongous room that allows you to take advantage of his slow, telegraphed attacks. The rest? They're all in tight, cramped areas.
If you return to the Undead Asylum after the tutorial, you'll find out that Oscar wasn't kidding when he said he would Hollow soon. He's not quite as tough as a Black Knight, but he's quick, smart, and leaves very few openings to attack. Adding to that, his sword deals magic damage, which means you can't just turtle through his attacks. Killing him nets you a very nice shield.
Royal Sentinels in Anor Londo. Regular Sentinels are nasty already, but Royal Sentinels are brutal. They have all the power of the Sentinels, but even more HP and the ability to use the Emit Force and Heal miracles. Emit Force will knock you flat on your ass if you're in range, and they love to use Heal just when you're about to finish them off. To add insult to injury, they spawn in the hall right before Ornstein and Smough, meaning that while you're trying to summon your co-op partner, they'll be smashing around trying to wear you down.
Heide Knights are the sequel's answer to the Black Knights. They aren't as big or strong, but they are more agile. One can be found in one of the game's earliest areas. Defeating this one nets you a decent sword for the early-game that can still be viable in the end-game if it's properly upgraded.
Anything that pops out of the white Monster Gates in Rune Factory: Tides of Destiny. Thankfully, unlike other Monster Gates, they don't automatically summon monsters when you get near them. If you manage to destroy a white Gate, however...
Despite being relatively easy overall, Golden Sun: Dark Dawn has a Brutal Bonus Level, and nearly everything that lives there is tougher than most of the game's bosses. Great Dragons are generally considered the worst of the bunch, and they like showing up in groups.
Opoona is full of these, as part of the game's general love of toying with the Sorting Algorithm of Evilnote As much as can be done without throwing off the game balance, anyway.. Although many areas have enemies in them who are stronger than usual, here are the most fitting candidates, in order of doomitude:
The Shredder, which is found only in one room directly before the boss in the Ruined Dome area. It has about five times as much HP as any other enemy in the area, and has more defense, too. However, because it's rare and in an area directly before a boss, most players will simply zip through the room without encountering it, and won't go back to it until an NPC encountered later on specifically clues you in that it's there.
The White Monk, found in the Sage's Tower, has far more HP than a normal enemy (over a thousand, which is more than most bosses), and its attacks, although not too punishing, are still something you need to be careful of. However, one of its Randomly Drops items is a big defense-boosting equipment only otherwise obtainable through a lengthyCollection Sidequest.
The Salamander has the most HP of any non-boss encounter period, and its attacks are murderous. To make things worse, it's often flanked with bombs (just about any attack that accidentally hits them will make them explode; one alone will more than halve your HP), and you can encounter it barely halfway through the game. There's quite a disparity in levels between when you can first encounter in and when you're actually ready to encounter it. Thankfully, it resides only in the optional Bonus Dungeon.
Deadliest of all is the terrifying Apocalypse II, found only in one small room in the Very Definitely Final Dungeon. It's insanely fast, and bombards you with laser attacks that knock off massive chunks of HP. Its defense is maddeningly high, and its HP is far too high for what its defense is at. And you have to beat it in under 2 minutes. Did we mention it's likely that you'll fight more than one at once, when one alone is more than enough for a Total Party Kill? Thankfully, it does give out heaps of experience, and brings you closer to 100% Completion.
The unique monsters in Xenoblade. All of them are tough enough to be considered bosses, and the sole distinguishing visual characteristic some of them have prior to being targetted is being slightly to much larger then the normal enemies in their vicinity. It's only after targeting them and seeing their level, odd name, and fancy info window that you can know for sure. They're also almost always aggressive, even if they're of a normally passive monster type, so one who has enabled the option to see monster info from a distance can potentially identify them in this manner, as well.
The most jarring example isDespotic Arsene, a level 108 bunniv that looks no different from the far weaker level 28 bunnivs in the same area, and is capable of smacking your party for over 10,000 damage (HP caps at 9999).
In a slightly more mundane example, it should also be noted that nearly every area in the game will have otherwise-regular monsters wandering around that are usually thirty levels above the party's level when you first enter that area at the very least. At least you'll know where to go when you need to level grind later.
Albion brings us The Fear (article included in the german version), and the Animal, as boss fights halfway through the second major dungeon in the game. They are quarding a key and a passage to the next level respectively, and have a lot of buildup to their respective fights, with the characters actually commenting on them. The Animal especially is considerably powerfull and fast, and can deliver massive blows and even critical hits. It's a standard enemy in all dungeons. In fact, the one you first fought is actually a lot WEAKER then all later variants. Thankfully, being supernatural creatures, means that they can be instantly removed from the field with a spell that is unique to the caracter who joined you prior to first encountering them.
In .hack, using Data Drain on an enemy turns it into a level zero critter. Except for The Guardian, which then turns into The Bracelet, a lv90 monster that has every top tier non-summon elemental spell in the game, and sometimes manages to cast two spells at the same time. Many a player thought it'd be safer to defeat it with physical attacks. Hoo boy, were they wrong: his basic attack is fast and strong enough to kill pretty much any character other than Helba in a matter of 2 to 5 seconds.
Mega Man X: Command Mission has the Meltdown. If you play the game with frequent backtracks to Gaudile's Laboratory to grind in the Eternal Forest, you might run into one at a moderately high level. However, if you play the game straight through, you'll start running into them in Chapter 7's Vanallia Desert. They have absurdly high HP, Armor, and Shield stats compared to other enemies, and have a One HitTotal Party Kill that they unleash after three turns in the form of a nuclear explosion that deals 9999 damage to your entire team. It's strongly advised to just run (meaning Zero is a bad choice to have in the party, as he hardly ever runs).
OFF has the Pastel-Burnt, which from outside battle looks just like any regular old Burnt, and confronts you like one. He also looks quite similar to most of the Burnts in the area, and even has similar attacks. The difference lies in the HP: It has tons and tons and tons of HP, which never seem to run out, perhaps more than one of the earlier bosses. Many lose a couple add-ons to this one after underestimating him, and get confronted with an enemy who simply refuses to die. He also has a few mook-making tendencies which can be taken care of with the add-on you got earlier, but will be your end if you don't.
The Denpa Men series has several. In the first game, if it looks like it's going to kick your ass,it probably will. There are many, many offenders (Golems, Windbugs, Dragons when at low levels), but among the worst offenders is the notorious Hydraplant. It attacks twice per turn, has tons of HP, can breathe various stat-affecting gasses, and absolutely loves to spam an Earth-type hit-all attack that can easily decimate all but the sturdiest Denpas in your party in one go—let alone two of them per turn! And they have upgraded versions.
In the sequel, Hydraplant got a massive downgrade, but Windbugs and Golems retain many of their former glories. Golems were even made stronger, since they're no longer weak to Light and Water-type attacks.
The Nazgul in the GBA version The Lord of the Rings The Return of the King. They spawn alone or in a group of 2 or 3 if the Eye of Sauron on the upper right corner fills all the way , which means they can be faced very early in the game. They are easily the strongest enemies in the entire game, being tougher than even the Witch King, their own boss. Not only do they have a very high HP, they also have a ridiculously high defense, causing almost every attack against them fail, unless the player is of extremely high level. Top it off with the extremely high damage their long reach attack does and you'll find any attempt to melee them is pretty much suicide. Their drops are not exactly worth the effort for "killing" them either, running away from them is usually the best option. On the other hand, at max level, they are the only enemies in the game to provide any challenge.
Pi'illodactyls in Mario & Luigi: Dream Team. They randomly spawn as a background enemy in battles on Mount Pajamaja or Somnom Woods (the latter of which gets their stronger recoloured versions), and can be mostly ignored. Except when you hit them with a Taunt Ball to bring them into the foreground, you realise the hard way they've got about three times the stats of anything else you fight in the area (except the boss), have about three or four hard to dodge attacks that can do plenty of damage and can theoretically wipe out your entire group. Heck, they're even harder than foes you fight about 10 hours later! Have fun.
Summoners in Fable I. The only saving grace you'll get from them is that they appear near the end of the game and you'll never fight more than two at once. That's where pleasantries end: they can't be staggered, have a fair share of unblockable attacks(including a ranged, AoE one that additionally - a rarity - turns off friendly fire), always appear with a few Minions and have tons of hp. If you manage to kill it, it explodes after a few seconds, further damaging you.
In Robopon, near the end of the second game, the Marvel Lab where Dr. Don and his assistant Sam take refuge contains a special group of Robopon in a certain room that appear at random. Defeating them may get you a medal that can be used at Play-Land to play extra minigames. The main problem is that the group is highly leveled and will wipe the floor with you the first time you run across them unless you come prepared. There is a Dragon Robopon in the past version of Delica Castle that is the same type of battle.
A feature of every dungeon in the Hyperdimension Neptunia series is at least one Risky Foe. These are identified by an orange dot and the minimap and will wait for you to start a fight, but are typically much stronger than the next few bosses you'll encounter after they first appear. It's worth coming back to defeat them later, though, as they're typically linked to sidequests and (depending on the game) are connected to some sort of progression system.