The original Street Fighter had Sagat as the final boss, who was not only the most powerful iteration of Sagat in the series, but also capable of knocking off more than half your life bar in one hit. And to top it all, all the now-standard Fighting Game special moves like Hadoukens and such were considered secrets at the time, with very few knowing of their existence, let alone the exact command to do them. And even then, Sagat could stuff fireballs and hurricane kicks cold. No tick damage, no knockback.
Balrog / M. Bison (Boxer) loves his Dash Punch. A lot. So much so that if you beat him once he gets pissed in Round 2 and does a barrage of instantly charged Dash Punches and Uppers. 26 times in a row. Afterward he waits and does other normals...for all of about 3 seconds. Then he resumes. Your only option here is to low block and die. Not or die. AND die. Because the frames of his Dash Punch never give you an opportunity to strike. If you have less than 25% life, you are FUCKED. End of discussion.
Vega / Balrog (Claw) likes to jump on the cage in his stage all the damn time. Oh, and he is very fast and unpredictable, and scores quick and very damaging hits against you. And when he gets off the cage, he ambushes you. If you narrowly dodge it, well, he follows up with an unseen strike. A special mechanic was even built in to his stage so if you played as him on that stage, you could do it too. In Super, however, the move is no longer available to the player, but the CPU can still do this.
Sagat returns from Street Fighter, with some new moves under his belt. Not that it matters because all he does is spam Tiger Shots all day. And if you jump at him he will do a psychic Tiger Uppercut. The AI in Champion Edition, strangely, never uses the Tiger Knee. Hyper Fighting fixed this, so now he will occasionally do a Tiger Knee up close...then tick throw you for the win. He also has one of the largest hit boxes of the original characters, besides Dhalsim of course. His kicks and Tiger Uppercut are difficult to evade.
M. Bison / Vega (Dictator) is this type of boss in the sense that there is absolutely no way you can predict what he will do. His AI pattern is completely randomized and will surprise you at every turn with a high-priority attack via command-reading. Thinking of doing a fireball? Head Stomp. Shoryuken? He'll Scissor Kick you right out of it. Hurricane Kick? Psycho Crusher.
Akuma/Gouki from Super Street Fighter II Turbo was this type of boss in his first appearance; he could teleport, was fast, did massive amounts of damage and could shoot two fireballs in mid-air. Furthermore, the secret playable version of Akuma/Gouki was less powerful than the boss version, though still so broken that he's always been banned from Tournament Play.
Apparently someone at Capcom decided that Akuma wasn't powerful enough, and thus Shin Akuma from the Street Fighter Alpha series was born. He regains the double air fireballs from Super Turbo, deals double damage with all of his moves, his teleports are completely invincible, and his Raging Demon now goes all the way across the screen.
Street Fighter Alpha 3 had M. Bison, whose Psycho Crusher attack is quite different between normal and boss versions in that it was huge and if not blocked did incomprehensibly high damage, and his teleport has 0 lag. The only way to hit him is to counter all of his attacks, which requires mind-boggling amounts of skill. Also, you can't continue if you lose to him.
Gill from Street Fighter III is incredibly hard to beat in one sitting. Projectile attacks that are much stronger than any of the main characters, a pair of special attacks that ate up screen real estate (and most characters' life bars, even when blocking), and the ability to fully revive himself after being knocked down make him a particularly controller throw-worthy boss.
On top of that, while you only have access to one of your Super Arts at a time, Gill can use all three of his. Just about the only upside is that during Resurrection, Gill is wide open, and a single hit stops the attack (although he also has a force field, so getting to him isn't easy) - so it's pretty likely he won't get back all his health. In addition, Resurrection shuts off Gill's Super Meter, so it can only happen once a round, for what it's worth.
Seth is the half naked man-cyborg Final Boss. He seems like a pushover during Round 1, but then in round 2 he suddenly starts using his special moves that he copied off of the other characters. He also starts spamming teleports around like crazy and with such accuracy that you'll usually end up facing the wrong way and eating a Spinning Piledriver. Still, there are ways to get around Seth's omniscient AI.
If you fulfill certain conditions after beating Seth (provided you actually get to fulfill them), a slash will suddenly appear through the victory screen and a silhouette appears. If you get 2 perfects and don't continue, you fight Akuma. If you do that while also getting 5 first attacks and 3 Ultra finishes, you fight Gouken. Both of them are cake compared to Seth, though.
Super SFIV takes it up a notch.
Seth starts using special attacks he copied off the other characters as early as Round 1. If you survive that, Round 2 unlocks his super and ultra moves. And he can pull off ultra moves twice in a row straight, with no recovery time. It's practically a Luck-Based Mission. However, if he has Ultra 2 he will always use it as soon as he gets up, no matter where you are. Be thankful Capcom did that. And when you finally get to play as him, he takes twice the normal amount of damage! Yes, his defense is the lowest in the game.
And if you fulfill the conditions necessary to fight Akuma after beating Seth, you fight Shin Akuma, who is Akuma in his 7th color palette (purple gi, darker red hair, reddish skin, basically Alpha Shin Akuma). Yes, He's Back, and more infuriating than before. He has 1000 HP and stun (same as Ryu), has his double air fireballs (normally an EX move) as a normal move, has an invincible teleport, and not only does his regular Raging Demon go faster and double the range it normally goes, but the Ultra version goes even faster, and across the entire screen. His Ultra 2 also hits on the very first frame, making it near impossible to dodge at close range.
Likewise, fulfilling Gouken's conditions gives you Shin Gouken, which is Gouken wearing his 7th color palette, making him look like the way Sheng Long was depicted (all grey gi). Many of his Specials now have armor break properties, and his Hadokens (including Ultra 2) are already charged to the max level. If you get hit by his Hadoken in a corner, blocked or not you WILL be trapped in the corner as he spams more Hadokens, safely chipping lots of life from you or outright taking away half your life in Hadoken combos if God forbid he tagged you unblocked. His Sengokugoshoha (the dashing palm attack) is also MUCH faster and has more invincibility. He may not be the worst boss ever, but you can't sleep on him as previously implied.
Arcade Edition ups the secret boss count to 4. But first the bosses proper:
Seth uses ALL of his moves, including Ultras and Supers, in round 1, and in round 2 he does combos which professional players already know, such as jumping MP into Toe Taps into Dive Kick for a reset.
Fulfilling the conditions for Shin Akuma and Gouken while beating Seth with a Super or Ultra will give you Shin Evil Ryu and Shin Oni, respectively. Shin Evil Ryu can have more than 1 Hadoken on the screen at the same time, has a more invulnerable and longer teleport, and from that teleport he can cancel it into any move he wants, including his Raging Demon and Ultras. Shin Oni's Hadokens are now already charged, and he has a vicious AI pattern that puts all the other bosses to shame. And they both have normal character health and stun (1000).
Juggernaut hits like hell and took a few blows to remember he had a hit stun. Just to put into perspective for people who didn't get it about Juggernaut. Many people argue that he is harder than Magneto, and with reason: In this game, he is a LITERAL JUGGERNAUT. If you wanted to die fast, you just needed to make your Full-special-bar-super-duper-stringy-combo. Juggernaut will take his time to do a full charged attack just because he won't flinch, no matter what. This works for hilarious effect if he starts using his Bum Rush while you are spamming him with Optical Blast at the farthest distance possible; He will PLOW THROUGH THE BEAM and will reach you with enough momentum to cause massive damage.
Magneto's AI is complete bullshit and seeks to royally piss you off at the worst possible time. He has a projectile which has absolute priority, can fly well beyond your character's reach (except if you're using Storm or Sentinel), and has a move which sends four magnetic orbs that home in on you and keep you stunned in the air if any of the orbs connect-you cannot block as was the case later on and the orbs move in such a manner as to block escape. To top it all off, he has two super moves, a trait which no other character has. One of them(Area-specific: the stage MUST be in the docking bay area-if the stage moves off, the move cancels) sends pieces of the docked Blackbird flying at you(The move itself costs nothing), while the other sends a bunch of energy pillars that cancel all projectiles. Also, Boss Magneto's X-Bar fills up automatically without him actually having to do anything, and will go from empty to full in the span of about 5 seconds, allowing him to use his super-moves all he wants. And he has an invincibility shield!
Dr Doom is absurdly good at keepaway. Plasma Beam has priority over a lot of projectiles and lingers long enough to make it difficult to jump over. Photon Shot will stop you from advancing at all against him. He can make things even worse with his flight and air dash, allowing him to perform his air projectiles which can very easily interrupt you and sport a huge range. Even knocking him out of the air is hard thanks to his erratic movement during flight. Not to mention that Specials and Supers will knock a gem off your character. Try to move at the wrong time, and Doom can easily knock half or more of your gems out without you even getting close to him.
Thanos follows up, and he begins the fight by immediately taking all of the Gems you've gotten. When the fight itself starts, you'll discover that his specials (Which he generally lacks, only having a ramming move, and a bubble that stuns you, being a pain in and of itself) his three most-abused ranged moves are actually NORMAL moves. While you don't have to worry about chip damage, Thanos's super gauge builds like CRAZY, meaning he can catch you with one of his six supers, which include having two stone slabs crush you to death (Reality Gem), hurling a miniature sun at you (Power Gem), sucking up rocks into a portal, and dropping them on your location (Space Gem), two which cause Interface Screw by slowing you down and reversing your controls (Time Gem and Mind Gem), and an energy chain that absorbs your health (Soul Gem). To make the Interface Screw ones worse, he can perform his other Supers while they are in effect, and he can easily trip you up by reversing your controls with Mind Gem, and performing Power Gem or Space Gem while you are still trying to get used to the control switch. While the AI isn't smart enough to realize that Thanos doesn't need the gem in question to do the particular super (Or maybe that's the point), it's a small relief, since unlike every other character in the game, Thanos will only lose a Gem when hit with a Super, as opposed to Specials and Supers. The other relief is that some of his normals, specifically the ground spike and rock throw ones, leave him open to air attacks, letting you get a combo in.
Cyber Akuma is basically Akuma but with a more infuriating AI, completely blown-out-of-proportion-overpowered moves, and a homing Rocket Punch just to add more injury to injury. His fireball/spinning kick/rising punch struck you and you knocked back? His Rocket Punch will hit you just before landing. Because, you know, when you just survived his special attacks, thus, failed to die in a glorious and flashy way, you deserve to be cherry tapped at long range.
He has Juggernaut's invincible bum-rush, can create missiles to prevent you from doing air attacks, has a larger version of Magneto's E.M. Disruptor along with his Magnetic Tempest, can instantly teleport, and to top it all off, he can summon random Brainwashed characters to do his bidding while he sits in the background healing himself. As if all that isn't enough to infuriate you, he has a constant Super Armor effect, which means even when you nail him with a Hyper Combo, he can just counter out of it by using one of his own specials, or worse yet, teleporting to negate a good chunk of your damage!
His 3 forms can be easily beaten by following his pattern of easily telegraphed specials and supers. The second form was particularly easy to beat, except when you have an all-melee team... what with having nearly no hit-stun at all and so able to use any of its attacks at you during your combos. Not to mention that if it decided to simply spam green-bubbles-of-death you can do little but get captured and receive its attacks in the ass.
Also, the last form can be infuriating. Of the three he is the least predictable, does the most chip-damage, disappears all the time and has knack of completely vanishing from your screen and attacking from afar, where you can't see which attacks it is doing (and some of them can nearly kill an average character). Or, better yet, he may decide to just get out of the arena altogether and start spamming its ranged attacks from off-screen.
First, you fight against Galactus' heralds at the same time, while you can only have one character on at a time, and they have infinite-use supers. However, they share a lifebar.
After they go down, you fight Galactus himself, who has extremely high health and defence, and does a ton of damage with his screen-filling attacks. When the fight starts he'll go easy on you with mildly telegraphed but deadly strong physical attacks, one of which is a finger flick that counts as a Snap Back, wherein your current fighter is booted off the field and another one forced into play, a grab that must be super jumped or button mashed to avoid, and a vicious Megaton Punch. Once he's down to half health, depending on if you wailed on him hard enough, he'll stagger, signifying that he's not pulling his punches and starts using his Power Cosmic on you consisting of various beams. Hilariously his eye laser can be avoided by getting right in front of him, but his other lasers aren't so easy, two of which (A Beam Spam from each finger and an array of beams that cover the screen) have to be blocked if you're not using a character who can fly, and they still cause massive chip damage, pray for help you if you're using Zero, Akuma or Phoenix who have the lowest stamina in the game. Once you've hit him hard enough he's likely to use a Sphere of Destruction that can instantly kill you if you don't deal enough damage to stop him. Plus, if you lose against him, he destroys Earth (EARTH K.O.).
To make his SNK Boss status even more apparent, the Ultimate re-release allows you to unlock a mode where you can play as him. (And before you ask, it's single-player only, obviously) Put simply, even a novice player has to explicitly try to lose in this mode, which is easier said than done, as he wins if the timer hits 0.
Capcom vs. SNK 2 has both Shin Akuma and God/Ultimate Rugal, both of them the result of one absorbing the other's powers. Like any other SNK Boss, they're extremely difficult to beat and have overpowered super moves, but they actually follow the same rules that the player is bound by. They're playable and balanced for human vs. human combat because they take significantly more damage when hit. Their difficulty comes primarily from the fact that the AI will use every dirty trick in the book regardless of what difficulty setting is chosen. That being said, you know that a boss is going to be a nightmare when each one's opening involves absorbing the other. Shin Akuma's opening involves him absorbing the last of the Orochi power from Rugal's death, while God Rugal has Akuma over his head at the start of the match, then tosses him away like so much garbage. Note that both of these characters are SNK bosses in their own game.
In his first, red, spherical form he's happy to spam a jumping hammer strike attack and a buzzsaw special, and in some cases will launch homing missiles to get on your nerves whilst hammering you. He loves spamming his stock-stealing super wherein he exudes a red force field, steals a super stock from you AND crumples your character for a potential free hit. Put simply his first form prefers to Attack! Attack! Attack!.
His second form, the yellow, armed biped form is easier since his attacks are more easily avoidable, even his fire wave super.
His final form goes back to the red sphere, now with a large arm coming out of it. He'll be lobbing meteors and tornadoes a lot, and his supers are a lot more dangerous. One summons a torrential downpour of fire, though he doesn't use that often. Another is a sweeping fire wave, though his final super, grabbing you and blasting you point blank with a fire beam does tremendous damage if he connects it. To be nice, however, you at least get your partner character back if they were defeated in any of the previous rounds, with a small amount of health.
Gundam Vs Gundam NEXT had Kira Yamato in Strike Freedom (In EX Stage final, where you have to in single player not only obtain a certain amount of points but also not die at all) whom first attacks you in Strike Freedom Form, Then in his Meteor where he gets a set of new moves and an annoying powerful attack that will smash most 1000 class mechs before losing the meteor and enters permanent SEED mode, which mean he can HIMAT burst to his heart's content. He was available in the next update but lacked the Meteor ability and can only go into SEED mode for a limited time. Some people thought he was worse than Devil Gundam, at least he stood still.
Also, his normal attacks are not to be sneezed at, his charge shot is pretty much dyname's sniper beam upgraded to hit you instantly and if you get caught in his melee, he will deliver an 5x Issen followed by Dragoon spam. This becomes painful when you fight against Destiny as well who has level 8 AI to back it up and denies your precious charge shot attacks.
WaDom earns the SNK boss award, a constant melee involving its legs, a counter grab. and you gotta kill two of them. Or the stage with Char, Quattro and Sazabi boss stage. Char carves you a new one with his speedy melees, Quattro does you in with its Wave Motion Gun and Char spams funnels and the beam shotgun.
Extreme Vs has the Extreme Gundam. Normally, he's tough but manageable, but in Tachyon Phase, with its heavy focus on melee, he gets this honor. Hyper-aggressive, nigh-undodgeable melee combos, a stun move that gives you maybe half a second to block, and the ability to supersize his sword in an instant. Even if you try to avoid 80% of his attacks by keeping your distance, he has a dash that lets him outrun any other suit in the game.
Power Stone has Valgas. Aside from the fact that beating him may require several tries with difficulty set to 1 (with a maximum of eight), what makes him so cheap is that not only his grab can make you lose two Power Stones at once, but said stones also tend to bounce out of your reach and right next to him, with him usually entering his Super Mode while you're still getting back up. The fact his One-Winged Angel is actually weaker than him (with obvious results: "Final Valgas" can be easily beaten at the first try) shouldn't surprise anyone.
Darkstalkers: The Night Warriors has Pyron, an Energy Being made out of fire who will put you on fire very quickly. He's fast and when combined with his teleport can make him very difficult to catch, plus he deals very high damage and has a projectile that takes up a large portion of the screen. When he became playable in the next game he actually didn't lose many of his tools, however.
Jedah in Vampire Savior: The Lord of Vampire can be tricky, thanks to his wheel attacks, flight mode and long normal attack range. He also has some incredibly damaging supers and another reason you should beat him quickly. but from the get-go the player has access to just about everything the boss character is capable of.
Star Gladiator's Bilstein is one evil bastard in the True Final Boss fight of the game (in which you must get to him from within a specific time limit or else risk getting a false ending). This form of Bilstein, called Ghost Bilstein, is an overpowered and unfair boss (imagine KOF '94's Rugal having the POW Meter maxed out and that it stayed on for the entire match!). His broadsword has a much larger range and that any strike from him can literally shred a huge amount of health from your character. His Plasma Revenge is very brutal and that it can outright kill a character if their health is very low. Also, he can't be ringed-out and that he seems to have a nasty habit in moving around real fast. Lastly, Ghost Bilstein has an exclusive move from within this form in which he summons an unblockable wave of Plasma explosions throughout the entire ring and much like the Plasma Revenge, these explosions can kill your character in an instant if their health is low. By the way, you only get one shot when fighting against Ghost Bilstein and that you have to defeat him in order to see your character's true ending. Losing to Ghost Bilstein gives you both an automatic bad ending and a game over.
From Mega Man Battle Network 5, Double Team DS, we have Bass XX...with 4000 hp, ridiculously overpowered attacks (his Darkness overload does at least 700 damage!), and a regenerating aura that takes 150 damage to get rid of for just a few seconds, he is EXTREMELY difficult to defeat.
In the Asura's Wrath DLC Lost Episode 1 and 2, Ryu and Akuma can be quite frustrating in the Street Fighter-styled portions of the DLC on the Highest difficulty and can do K.O.s with just a few good combos. They are really hard in the Asura's Wrath styled portion of the game, too, but only on Hard mode diffculty. It can, however, be made (even) worse with the Mortal Life gauge.
Jojos Bizarre Adventure Heritage For The Future's Super Story Mode has some exclusive enemies that can bring a lot of pain if you're not careful. Death 13 is an example, as he's a annoying flying character and has good range and power with his scythe.
Vanilla Ice, who is just the sub-boss, is actually much harder than the final boss. All he does the entire match is vanish, appear on the corner as a void ball that crossses the screen in a erratic pattern and then fall from the roof. This attack is unblockable, takes 1/5 of your life (yeah, five hits and you're history), and sends you to the wall. If you don't dodge, you'll miss the only opportunity to hit him, which is when he's falling, and that is just a split second before he recovers and starts the pattern again. Every now and then (and surely, if he's left alone at low health), he will use one of his two supers, one where he make three huge voids at random points on the screen, and other where he circles around the entire arena while shaking it, which is very hard to dodge.
The final boss, Dio Brando, actually subverts it. In the first round, he will just teleport and use his MUDA-MUDA while randomly clapping, and if you're at full screen distance he will use his Space-Ripper-Stingy-Eyes, which is unblockable, but he doesn't even bother to block or counter your attacks. In the second round he takes off his coat and starts actively using his stand. While he is very aggressive, he still plays by the same rules of the player.