God Hand does this when you fight yourself in Stage 51 of the Fighting Arena.
The Fighter boss in Kirby Triple Deluxe's fighting subgame. At difficults other than Easy, he will spam the down-forward-punch attack faster than any human can conceivably input the combo.
In the original Advance Wars, the final "boss" CO Sturm is an unlockable character to use in Versus mode. His units do more damage (though they have weaker defense) and his CO power makes a meteor smash onto the largest concentration of units in a 5x5 diamond shape, which does 8 damage (out of 10). Versus mode Sturm however has a greater defense and less attack power, and aforementioned CO power does just 4 damage.
In Advance Wars 2 Sturm now has an insane defense as well as insane attack power. He is either banned or tag teamed played in 2 vs 1 matches.
Though oddly enough, his units receive a larger move penalty when it's snowing than any other CO does (only comparatively, he has the same movement costs as everyone else, but given that he has no movement penalties usually, it hits him a good deal harder than other COs). However, since there's only one CO (Olaf) that has this as his powers and the COs you take into the final battle are determined by certain conditions and not by choice.
You could choose who you take into the final battle in Advance Wars 2 (the game where Sturm is really, really cheap, but still). And for the weakness to snow, since 1) the only CO able to use that (Olaf) is not one of the strongest or easiest CO to use (to say the least) ; and 2) the snow will bother your troops as well...Let's say that's not a painful weakness for him.
And in Days of Ruin, we have Caulder. In a game where CO powers have been nerfed compared to previous game, his CO power is considered even more powerful than Sturm's. Simply put, it's a 3x3 aura that grants massive stats boost and regenerate 5 hp per turn for all of his units in it.
Various RTS games face a campaign only "boss" unit, or the enemy has some special thing(s) that is unique to the campaign.
In the original Command & Conquer, the temple of Nod at the end of the GDI campaign can fire multiple nukes during the mission. This is compared to the nuke silos players can build, which fire one nuke and can never be used again.
Tiberian Sun: Firestorm has CABAL's army fought in the last mission of both campaigns. CABAL fields mostly Nod units, but also includes CyborgReapers which can render most infantry helpless and make for mean anti-materiel weapons. Once you've finally wrapped up the multitude of bases that span the entirety of the very large map, CABAL himself is guarded by the titular Firestorm defense system (think "literal firewall"), which in a rare instance of smart villainous planning holds its power source within the 'Wall. Take that out and CABAL deploys the Core Defender. It can shrug off your Ion Cannons with little effect, can kill anything in two shots or less, and will completely wreck your shit unless you're prepared for it. Its one weakness is the aerial option.
In Tiberium Wars: Kane's Wrath in one mission you will face up to 3 MARV Tanks, two of them at once. Players can only build one MARV unless they capture a Construction Yard of an opposing GDI faction (it has to be a different GDI faction, not just any one mind you). Inverted during the final mission, where it is possible to build 3 Redeemers, but it's highly unlikely that you'll use them since the level is going to end one way or another at that point.
You can build 2 MARVs but not in the campaign. In the Global Conquest mode, as GDI you can deploy the most powerful army, which will include a MARV by default. During a mission, you can build another MARV. You can't keep the second one beyond the mission, however. This applies to all epic units.
In Tiberian Twilight's final Nod mission the final 'boss' is the enormous Arcus Bomber. In the introductory cutscene it eliminates your allies' Crawlers and can obliterate most of your forces with just a few shots. Since the game unlocks more advanced units as the player gains experience, the player may not yet have access to the only units powerful enough to do any real damage making the game impossible to complete without spending hours player multiplayer and Skirmish mode games in order to unlock the necessary units.
Blizzard had something of a fondness for super strong units in Warcraft III. First case is in the final level of Orc campaign where you face off against Chaos Orcs - essentially your own units with far more impressive stats, and a unique damage type that does full damage to everything. The final level of the Night Elf campaign pits you against an Undead enemy that cannot be conquered and fields units that players normally cannot control, in escalating numbers. Among them are Infernals, which are immune to magic and deal damage to all nearby units every second, and Doom Guards, which while weaker than Infernals are still stronger than any ground units you can field. The computer will also send hero units with some unique abilities at you, most notably Archimonde, who alone is capable of tearing you apart. Thankfully, he only shows up in the last couple of minutes and your task is to merely delay him. Incredible stats, unstoppable skills, and Divine armor (only vulnerable to an attack type normally found in high level creeps). In the unlikely event you can kill him once, he has an item that revives him with full health and mana.
This was kind of the trend after Warcraft 3: Reign of Chaos, where the campaigns would always end in some overly powerful boss that was a modified unit. Not surprisingly, this eventually gave way to World of Warcraft, whose MMORPG style basically makes this mandatory for its Raid Bosses.
The original campaign in Warhammer 40,000: Dawn of War had you fight a Deamon Prince at the end, who was way stronger than even the game's unique super units. Even when he finally becomes a usable unit in later games, his damage got nerfed from the unholy damage Sindri will wage.
Considering the game it's based on, it's probably still better to fight it here than the original, and infinitely more survivable than being a character in the flavour text....
Dark Crusade and its sequel Soulstorm both had this whenever you attacked a stronghold. While you had caps on many units limiting their deployment, no such exist for the enemy. In the assault on Victory Bay, expect to face no less than 4 Leman Russes and at least 2 Baneblades, the former of which can and will be rebuilt until the enemy is dead (normally, you're only allowed 2 russes and 1 baneblade). Stronghold missions also often give Honor Guard Units to the AI in ways you can never dream of, such as entire squads of Daemonkin Obliterator, or Honor Guard Predators.
Soulstorm's Sisters of Battle stronghold has a version their Living Saint super unit that can't be damaged until you destroy four icons on the map, and the AI is smart enough to keep it near one.
And in Dawn of War 2, the extension Chaos Rising tops it with a Great Unclean One, a Damage-Sponge Boss with devastating attacks and that can see infiltrated units. He also has an aura of decay that will automatically detonate any explosives you have Cyrus set up, forcing you to get up close with the abomination.
King Famardy in King Of The Monsters 2 (which, surprise surprise, is made by SNK). He is ridiculously huge, moves very fast, can use the projectile attacks of every other bosses in the game and he is the only one that can hurt your character simply by touching you, whereas being touched by the others bosses would atleast locks you in a random but potentially successful grapple.
Midas from Agarest Senki. Doesn't play fair with his Limit Break meter. Has attacks that one-hit kill all characters in a 2-cell radius, too much HP, regenerates health at an absurd rate. Has a Limit Break that can guarantee a Total Party Kill if you party isn't spread out far. And did we mention you fight him halfway through the game, before many of its Game Breakers become available?
Kingdom Hearts's Bonus Bosses often edge into this, due to their abhorrent attack power and incredible speed. One of them even has attacks that bypass the abilities to stop instant/combo induced death, this is all made much worse by the rest of the game's relative ease, making sure the player's blindsided by the Difficulty Spike.
The North American and later revised Japanese releases of the first game feature Sephiroth, whose attacks not only come out fast and hard, but also has absurd range. His Heartless Angel brings you down to one HP and depletes your entire MP gauge. Unlike some other bosses, he can actually use one of his desperation attacks before he actually gets desperate which is basically his version of an Omnislash. You can only hope to block it, or if you have near superhuman reflexes, dodge each and every strike with absolute precision. His actual desperation attack, Supernova, can hit you from anywhere when he actually throws it at you, and it can't be blocked. During his desperate state, he starts pummeling you with spinning strikes which he whips out immediately after coming out of a teleport, and it's almost always behind you. And when he does so, he leaves behind a wall of Shadow Flares. Some argue that this version of Sephiroth is the hardest incarnation yet. Also, the player has to fight him one on one.
In KHII, he uses the Omnislash-like attack more frequently, especially to stretch out the part where it's his NORMAL ATTACK. Unless you've leveled up your Drive Forms up to this point, be prepared to eat a lot of Heartless Angels because he friggen floats out your range when he powers it up this time around. When he gets desperate, he goes so far as to actually SLIDE BEHIND YOU when he attacks. He also tends to poke you by quickly gliding around the arena and then smacking you. Lastly, his Reaction Command attack, while easy to see coming from a mile away, going so far as to start every bout doing it, do NOT get hit by it. It will hit you from anywhere and everywhere, so be sure to have your feet planted firmly on the ground because you CANNOT block it in the air. However, the real hammer on the nail is the fact that even though Goofy and Donald are explicitly present before AND after the battle, they are completely absent during it, so no Drives or health refills.
Then there's KH Final Mix's Unknown/Xemnas, who bashes you with swift and powerful strikes and uses a multitude of powerful spells that will absolutely demolish you and he is almost always constantly doing so. He can suspend energy bolts in mid air while, after a second, come at you in a rapid fire fashion, generate large energy orbs AND can guard against your attacks by putting up a large shield which can also damage you and knock you back. He also has an attack where he places a unique status ailment on you that will gradually drain your health unless you use the proper command when prompted to. You will be doing quite a bit of rolling around until he bothers to actually give you an opening. However, unlike with Sephiroth, the player does have Donald and Goofy for the fight.
KHII Final Mix has two of these, unfortunately. First up is the full Roxas fight. Unlike the playable version of Dual Wield Roxas, this guy is completely batshit insane and uses his real powers to their fullest.. His standard attack combo consists of him constantly shifting left and right as he attacks and before you have a chance to immediately counterattack, he jumps right back and comes at you. After recovering from any attack, whether or not its a combo, he will retaliate immediately by jumping in the air and coming at you with you a rolling attack that will track and hit you, no matter how far you are. He also has his own version of the The End Reaction Command and if you can get it, you can snag his Keyblades from him to amp up your attacks. The catch however, is that he'll actually become even more aggressive and start throwing friggin laser beams at you until he manages to steal his Keyblades back from you. But at this point however, he'll start buffing his attacks with constant beam attacks in varying patterns. Not even getting into his desperation attack, he has another attack where he constantly spams Strike Raid while constantly buzzing around you. And it hurts. A lot
Ugh...the Lingering Will is an absolute nightmare. This is the only superboss in the entire series who CANNOT be knocked out of his attacks and at the beginning of the round, he's usually flying all over the place at high speeds at which Sora can't even hope to match. Invincibility frames on every attack he does. They all involve his Keyblade taking on a multitude of forms and they come out quick. Even when he's running straight at you, you can't hurt him. At all. Your only bet is to hit him after an attack. He has actually has an attack that breaks him out of any your combos by immediately countering with a whip attack which you cannot get out of. He has two variations of a magic seal attack that either seals your attack or magic commands, forcing you to hit LW a number of times to break out of using the command that wasn't blocked. And then there's his desperation attack that requires a specific set of maneuvers to perform to survive it, because it's not only lengthy, it's pretty much guaranteed to kill you. And the best part: His number of health bars span the size of the longest possible gauge in the game, surpassing even Sephiroth.
If you thought the Lingering Will was bad, wait until you fight Vanitas Remnant. While he has only one bar of health, be very very prepared. He has an absurd amount of defense and even if you managed to max out your character, your combos won't be doing a lot of damage like on other bosses. He is basically a souped-up version of Vanitas at the end of Ven's story, his attacks do fatal amounts of damage, usually almost one hit kills, even if you've leveled up excessively. He also has a new attack where he encases himself in an invincible sphere and launches shadowy versions of himself at you which fly quickly at you and deal insane amounts of damage and if you get hit, you'll be inflicted with Blind which obscures your line of sight almost entirely. Don't even try to use Cure spells, because he will go right ahead and do he same, so actual potions and exlixirs are essential. Like an actual SNK Boss however, he's not very smart and will blindly run into Mine spells without changing his path.
And then there's the other secret boss introduced in the North American and Japanese re-releases, the Mysterious Figure. Drop all of your uberpowerful commands and spells in favor of quick ones that offer invincibility frames because this guy will ruin your day hard. Everytime he is in motion, running or walking, he is constantly warping and darting around, so forget your Shotlock. Instead, don't use Shotlock at all because he actually has access to the Heal Block command which transfers any usually incurred damage into health. He has a long combo not unlike Xemnas, but it is far far longer and it WILL deplete your health to zero, unless you have the Chance abilities equipped. He also has access to a projectile version of Tornado that will literally blow every command in your immediate deck out of your body, forcing you to try and pick them back up while he finishes you off. Gets even worse when he jumps into the air and throws out an energy whip. If you get hit by this, you will assuredly die because not only does it almost take out almost all of your health in one sweep, he will not hesitate to spam it over and over again, AND it negates your Chance abilities. Aside from his Beam Spam attack and Doom attacks, he has the annoying ability to actually recover bits of lost health by turning back time if he gets hit by a powerful attack. And then when he actually gets desperate...
Don't even get me started on Iron Imprisoner, the constantly evolving SNK boss from the Mirage Arena. The Mirage Arena is designed for multiplayer, but they don't drop the difficulty if you try and tackle it solo and damn! Stage IV is the worst: absurd health levels, incredible attacks, trapping you in a flaming cage that'll kill you in three turns, and taking over the arena, holy crap.
And now Dream Drop Distance introduces us to Julius of all people. Unlike the preceding blade-wielding counterparts, he's all about brute strength...and is exceedingly effective at it. Basically every single action he does will hurt you. If you do not have a high-leveled character or Once More/Second Chance, you'll die quickly. When he's not charging at you with a barrage of punches that cover a lot of ground, he'll try throw his weight at you, whether it's a sliding elbow drop or a free fall from an elevated height and either can destroy the poles that allow you to do Flowmotion attacks. If he hits you with the latter, the currently selected Command will be disabled for a little while. Even going into his powered up state is designed to kill you since he summons lightning bolts that randomly strike anywhere and all you can do is block and pray. When charged up, his attacks become unblockable and gain an increase in range. He also only ever flinches after several hits. Fortunately, Julius isn't in constant motion like his Square predecessors and leaves himself open on two accounts, both usually right after finishing an attack and he only has one projectile attack (no magic spam). Since he only charges at you, you can pretty much repeat the strategy employed against Vanitas Remnant using this game's version of the Mine spell, Balloon. Riku stands a better chance surviving his attacks thanks to his unique action commands Dark Roll and Dark Barrier.
In the JRPG Dragoneer's Aria, to get to the Earth Dragon, you have to Battle against Ruslan L'avelith. While fighting against him, he can easily kill your entire team. Once you beat him and he joins your team, he's nerfed like hell.
Fire Emblem Thracia 776 is already the hardest Fire Emblem game in the series (or heck, it's probably the hardest game in existence!) Then along comes Chapter 22, which has several factors working against you as it is. Once you cross the second bridge, however, the first one collapses, and the mini-boss, Reinhart, starts attacking you. He has Daim Thunder, a weapon normally only available toOlwen, which allows him to attack twice, and has FOUR skills: Continue (randomly allows him to attack twice in one round) Ambush (ensures that he attacks first no matter whose turn it is), Duel (forces another round of combat without allowing the unit that just attacked a chance to heal) and Big Shield (will randomly block one of your attacks entirely). With all these power-ups, it is literally and completely impossible to beat this asshole without resorting to status effect wands, which are rare. Silence keeps him from using magic, so you can thankfully use ranged attacks against him (he also has a Brave Sword) but the most reliable way to beat him is to put him to sleep, and yet both options are only achievable with a M-Up wand or a Holy Water, since your wand user must have higher magic than he does, and all stats except HP cap at 20 in this game! Reinhart's mere existence might just cause your file to become unwinnable if you don't have Warp wands, which most people use to kill the real boss on the first turn (He also has Big Shield, so good luck with that!) and warp Leaf to the castle and seize it for an instant win, but then you miss out on the chapter's other goodies. In fact, the first house on the map gives you a Warp wand, as if to say, "Yes, you dumb fuck, that's how you're supposed to clear this chapter." To add insult to injury, you have to have the above mentioned Olwen talk to him to obtain a rare weapon. Oh, and during the course of this chapter, you have to deal with the combined leadership stars of Reinhart, Ceon, and CYAS. Cyas alone has 10 leadership stars, and together, all 3 bosses have 19 leadership stars. This means every enemy on the map gets +57 to hit AND evasion. These bonuses also apply to the bosses themselves, so...good luck.
Then there's Medeus on Lunatic Mode in New Mystery of the Emblem, who takes "blatantly unfair" Up to Eleven. He has all his stats maxed out, which equates to:
40 Skill (meaning a base critical hit rate of 30%, i.e. only a maxed out Luck Stat is enough to totally negate the chance of a critical, and a critical WILL kill you, no exceptions.)
30 Speed (by far the worst of the lot, this means he'll double attack anything up to and including Heroes [26 Speed] and looking at the previous points, you should be able to put two and two together. Yes, NOTHING can possibly survive 2 hits from him, meaning anyone with 26 or less speed who attacks him is already dead. )
Furthermore, he has a range of 2 spaces, meaning not even Archers are safe and any Staff users trying to heal a melee attacker will be in his attack range. Oh, and did I mention you have to deal with him AND 20 odd Bosses In Mook Clothing at the same time??
But, Medeus and Reinhardt are nothing compared to a Bonus Boss in Fire Emblem Awakening: Anna, from the Apotheosis DLC. The boss has stats far above your own maximum stats unless you spam Rally skills AND buy the DLC for the skill that can raise your maximum stats by 10. And of course, an absolutely broken skill set with Vantage+ (which allows the boss to always go first in a fight), Dragonskin (halves all damage), Counter (damages any attacker for the amount of damage they've dealt), Aether (a skill that deals two hits, one that deals regular damage and heals HP equal to half the damage dealt, and another that halves the opponent's Def), and Rightful God (raises skill activation chances by 30%. That Aether has a 65% chance of activating) And finally, you fight this boss after a marathon of the other bosses from the chapter who are also all ridiculously difficult. Thankfully, this map has the same difficulty on Normal, Hard, or Lunatic(+). It'd be impossible to imagine this any harder.
Magic: The Gathering: Duels of the Planeswalkers 2012 (a game based on a Collectible Card Game) has Karn. While most of the cards you can get for your decks can be described as "strong, but fair", Karn has cards in his deck culled from the Legacy ban list. God help you if he uses a Mox to Tinker for Darksteel Colossus on turn 2... your only response is pretty much Counterspell. Or concede. (Or Unsummon the Colossus.)
Arkazon, the end boss of the Shandalar computer game from the 90s, turned up with an enormous five-colour deck and would open with huge amounts of life and several permanents already on the field...sadly for him, he ended up a subversion due to poor construction and coding: the deck's sheer size and lack of dual lands, dedicated landsearch and so on made it extremely cumbersome, and the AI was not particularly impressive even for its time.
The final fistfight with General Kim in the true ending of True Crime: Streets of LA.
Starting in Armored Core: Master of the Arena, the Armored Core series would include a boss AC called Nineball Seraph. Most up to the point you meet this thing, all enemy A Cs are simply AIed controlled versions of A Cs you could build yourself if you really wanted to (except for an end boss in Project Phantasma, but Game Breaker machine gun made the thing a pushover), but Nineball Seraph is constructed entirely from parts you can't use. The thing is extremely fast, and has way more armor than an AC for its speed would allow, really strong machine gun arms that both have laser blades (if you use gun arms you can't have laser blades) that have a higher attack rate than yours, since it has two, and a couple of back mounted homing missiles that are very accurate and really hurt. For added speed it can transform into a birdlike mode that makes it even faster, though in that state it will only use its missiles. No matter how you build your AC, this will have you heavily outgunned and kill you a few seconds, even though your armor is fully restored before you fight it.
Kioh Gyoku's Final Boss is entirely unfair. Muse, as a playable character, is one of the best characters in the game to begin with. But that wouldn't be epic enough, so the designers did horrible things to her stats. The increase to her defence is at least understandable, since the AI sucks and she'd have killed herself before the battle really started if it hadn't been increased, but they overdid it to the point where the fight with her takes longer than the rest of the story mode combined. But the real problem is that her attack ranksnote every time a player uses an attack the rank for it goes up by one, making it slightly stronger. They normally start at 1 are increased, with her non-boss attacks at 12. Which is a serious problem, since, at that rank, her level one attack basically requires you to stream it across the entire screen to avoid it, and will most likely guard break you if you screw up. Which you probably will if any of her other attacks are on the screen. The fight basically comes down to hoping and/or praying that she dies before the A.I. Roulette decides to use that attack a thirdnote you have two screen-clearing bombs time.
Dynasty Warriors: Gundam 3: Knight Gundam at the end of the story mode. Assuming you're using a fully-upgraded and customized suit with a high-level pilot, you will still do only minimal damage to him, and he can kill you in two hits from any attack (that's if your defense stat is higher than 350... otherwise he One Hit Kills you). Also, Knight Gundam is one of those Gundams with a "Super Mode" that he enters into after using an SP attack. Except for this battle... he's in his Super Mode for the duration of the fight, and it never runs out. Good luck.
The Disgaea series usually averts this, as with the Absurdly High Level Cap most bosses are just the same as highly leveled and well equipped normal enemies; they're tough, but the follow the same "rules" as everyone else. Even some bosses where you must lose to advance the story can technically be beaten if you don't mind a Non Standard Game Over. But Disgaea 4 gives us the DLC battle with Baal; he has the power to get a free attack on your characters from any distance as soon as you remove them from the base panel. Since he's incredibly strong, this means he can literally kill your entirely party before he even gets a turn. They just die as soon as you try to use them.
His incarnation in Disgaea Dimension 2 is even worse. His stats are so insane it requires the abuse of mechanics to max out the game's stationary attack bonus to do any real damage to him, he's never resets, so as they fight goes on his attacks do more and more damage, along with now possess an Evility throughout the fight that grants him immunity to any skills used on him after the first time, plus his Evility from Disgaea 4, and after taking damage, he'll switch to other evilities, the last one which destroys your base panel. Thankfully, his immunity to skills resets everytime he changes evilities.
Crash Team Racing's final boss N. Oxide has access to a nauseating amount of surplus; to be specific he's unaffected by any of your attacks, when he's in front of you he drops Komodo Joe's instantly-exploding TNT Crates, Nitro Crates, Bowling Bombs, and Green and Red Beakers (moreso than the previous bosses) on top of being fast enough to easily catch up to characters that focus on speed such as Tiny and Dingodile. Adding insult to injury he leaves the finish line before you do ensuring that there will be a huge minefield between the two of you when you take off. In comparison the final boss of Crash Nitro Kart is a bit easier to outperform.
Strike Freedom in the bonus stage at the end of branching routes in Gundam vs. Gundam Next Plus. Has the same functions as the playable version but has a health gauge way longer than any of the bosses you fight in the game, at least as long as Devil/Dark Gundam's. He also has an exclusive attack involving a rushing attack with his Wings of Light and Super DRAGOONs. After he's sustained a good amount of damage, he'll immediately strap on METEOR and then shit gets real; dual plasma cannons that can knock you down in one hit, plus missile spam and his strongest attack brings both Beam Spam and Macross Missile Massacre together for a speeding wall of death on top of uber beam sabers. And to top it all off, his Assist is a METEOR-equipped Infinite Justice who will do the exact same thing when called on. If you've managed to hit him hard enough, he'll ditch the trashed METEOR and start fighting like "normal", except he'll have infinite SEED factor, giving him insane boost dashes, reduced boost usage and Full Burst Mode. Making this all significantly worse is whatever you have to fight before and during the battle with SF which are usually powerful suits like Wing Zero and 00 Raiser and if you followed a particular route to get to this stage, you have to fight all alone.
In Mega Man 8 Bit Deathmatch's single player campaign, normally bosses are considered "monsters" by Doom engine standards, there are a few bosses that are considered normal bots but with special weapons and stats; three are Bonus Bosses while one is a mandatory chapter boss.
The first Bonus Boss, Enker, runs around in an erratic pattern, causing Collision Damage if he runs into you, stopping ocasionally. If you hit him while he's stopped, it increases his projectile in power.
The second Bonus Boss, Punk may be considered the hardest. His normal projectiles travel at lightning fast speed, and he also has a hard to dodge ram attack that can take off nearly your entire health bar.
And the icing on the cake? Evil Robot, the V 3 A (Current) Final Boss. He doesn't only have invulnerability while attack, but he also has absurd attack patterns and can only be hurt when trying to tackle you, and that vulnerability frame is ONLY WHEN HE IS DANGEROUSLY CLOSE. Also, did I mention he combines two attack patterns when his health falls below 50%?
And now there's their version of Saxton Hale Mode. Suddenly, facing campaign bosses seems so easy...
Lord Bloodcrown, the Final Boss of Clash Of Heroes. He has double the hit points of any other boss in the game, attacks solely in devastating charged attacks (the charge spheres of which will intercept any but the most powerful attack, save for a small window between them) and he's stationary, meaning about a quarter of your playing field is useless). Not to mention you're forced to fight him with Nadia, who is likely to not even at the Level Cap when you face him and whose special attack is random, turning him more of a Luck-Based Mission than a Boss Fight.
The final two levels of the browser-based game Slime Volleyball: One Slime fit this trope. The second-to-last opponent, Psycho Slime, moves faster than the player-controlled slime or any other slime in the game. The last opponent, the Big Blue Boss, is substantially larger than other slimes (filling up most of its side of the arena an thus making it difficult to score).
Caius Ballad in Final Fantasy XIII-2 has an ability that lets him reset his "break" meter, which you pretty much need to fill in order to deal any kind of damage to him. He is the ONLY boss in the game that can do this (though he shows up multiple times).
Reshef in Yu-Gi-Oh! Reshef of Destruction has 40,000 Life Points (the player has 8000), three versions of cards that are limited to one for the player, and the God Cards, too, for some reason. He also starts out with the Darkness field, which powers up all his monsters, and with three Castle of Dark Illusions, switching the field to something more favorable is almost impossible without him switching it back. Nearly all his Monsters have at least 1800 ATK, which is something that's almost impossible for the player without heavy, heavy Level Grinding. Also, you fight him right after Sol Chevalsky (no slouch himself, with 20,000) and you can't recharge your Life Points. If Reshef can Summon Ra, who has a Cast from Hit Points ability that sacrifices nearly all his remaining Life Points to deal equal damage to you... game over. And with three Pot of Greeds, he WILL draw it, and with three Change of Hearts, he WILL get the necessary three Monsters to Summon it. Basically, you could be using an Action Replay and Reshef would still be an incredibly tough boss.
Z-One in Yu-Gi-Oh! 5Ds Tag Force 6 is the only character in the game who uses the Timelords (notthose ones). The Timelords are all pretty much indestructible, can Summon themselves easily, and have very potent burn, bounce, and spin effects that activate when they battle. Among the stronger ones are Michion, who halves the opponent's Life Points, Razion, which sends the opponent's entire Graveyard back to their Deck and does 500 damage, and Metaion, who bounces all your opponent's monsters back to their hand and does 300 for each one. You can't even fight back against them, because though they've got zero ATK, they negate all Battle Damage done to them. Your only saving grace is that he can't control more than one, and the Timelords return to the Deck at the start of Z-One's turn... unless he gets out Infinite Light Ain Soph Ohr (or even its lesser form, Infinite Machine Ain Soph), which handily negates those weaknesses. And it goes without saying that none of this is in the actual card game. The only Timelords ever released were Metaion and Sephylon, and obtaining the Timelords in Tag Force 6 is tricky at best at the stage when you fight Z-One. There are countless videos on Youtube of Z-One being pitted against other AI opponents and absolutelycrushingthem. The best part? Most of his cards are toned down from his appearance in the series.
Minion is a recurring mid-story SNK Boss in the Twisted Metal series. In a game full of relatively normal cars (minus the weapons, of course), Minion usually drives a freaking tank. The games usually give him utterly broken stats and (in the case of the first game) multiple special weapons. Furthermore, in most games in the series, you can unlock Minion either with a cheat code, through story progression, or by finding a hidden item in a stage; even though his tank is still one of the best vehicles in the game, it's seriously nerfed compared to when you face him as a boss.
In Twisted Metal: Black, Minion now drives a tanker truck instead of a tank, but when you face him, his vehicle has shields that must be beaten down. And he's still not the cheapest boss in the game. That "honor" goes to the Final Boss, Warhawk, an assault helicopter. A helicopter in a car combat game is just as broken as you'd expect, but on top of it, he also has shields. This is why he wasn't made a playable character — no matter how much the developers tried to nerf Warhawk, they couldn't find a way to make him exceedingly overpowered, especially in multiplayer. (They eventually did pull it off in the PS3 game with Talon, which didn't have Warhawk's lethal special attacks.)
The worst SNK Boss in the entire series, though, is in Twisted Metal 4. In that game, Sweet Tooth, a recurring character from past games in the series, serves as the Final Boss, and his special attack has been "upgraded" accordingly. The mere mention of it is enough to send any Twisted Metal fan into fury — it fires three orbs that go through walls, one of which fires missiles, another of which shoots flames, and (worst of all) the last of which fires an electrical bolt that pulls the victim towards them, effectively trapping him or her while the other two wail away. All but the most heavily-armored vehicles in the game will get shredded in seconds, and all but the fastest will be unable to escape them. There's a reason why this game (along with the previous game, made by the same developer) are considered non-canon by both fans and the developers.