Hey, here's a top 10 list for you challenge seekers out there.
Top 10 Hardest Bosses!
10. The Master of Darkness (Warcraft III)

Shameless self promotion time! This boss comes from my own Warcraft III mod, Hero Arena Underground. Since it's a multiplayer map, I wanted to create a boss that would be a challenge even for a full group. This guy erodes armor near him, summons four pet Nether Dragons, and can paralyze you with a bolt of darkness to bring you into a world of pain. I partially based him on Archimonde, the undefeatable final boss of the campaign. Suffice to say, I got what I wanted, and even with a full group of max-level heroes he can cause a wipe terrifyingly easily. On another note, designing deliberately overpowered bosses is really fun.
9. Boost Guardian (Metroid Prime 2: Echoes)

On the surface, this thing might not look like much. It's just a standard Warrior Ing that's stolen Samus' Boost Ball power. A few seconds of fighting against it, though, will tell you that this fight is nothing but standard. Like Samus, it can curl up into a ball and ricochet around the room. This is crazy difficult to dodge, and if it impacts you it deals heavy damage. It's immune to beam weapons in this form too, so you have to go Morph Ball yourself to counter it and drop bombs until it uncurls again. To top it all off, your health is constantly being drained by Dark Aether's toxic atmosphere, and there are no safe zones anywhere in the fight. The pillars in the room hold valuable health pickups, but you can't destroy them, only the boss can. If it takes one out at the wrong time, tough luck with that. Even worse, if you kill it while you're at low HP, the damage over time can finish you off before you pick up the Boost Ball.
8. Dullahan (Golden Sun: The Lost Age)

This headless warrior guards the ultimate summon, Iris, and will happily beat you to death for the right to use it. His Fulminous Edge deals wicked lightning-based damage, and he can also cast some high-powered earth Psynergy. His ultimate move, though, is calling the boatman of death, Charon. This works just like your Charon summon, dealing extreme earth-based damage with a chance on instant death. I once had it proc on my whole team at once. Also, he takes two turns per round and regenerates HP over time, so you need to deal with him quickly. I found that rushing him with summons is pretty much the only way to beat him.

He reprises his role in the sequel, Dark Dawn. He's got all the same moves as before, plus he can now use Crucible to turn your own summons against you, making him even worse.
7. Sephiroth (Kingdom Hearts)

Sephiroth is known for quite a few things, including being the villain of Final Fantasy VII, being hot, and being a brutally hard bonus boss in Kingdom Hearts. The first time you meet him, he'll likely take you down in one or two hits. Do a lot of level grinding, and you might be able to stand against him, if you're really sharp. He's highly mobile, immune to magic, his sword range is a lot longer than yours, and you don't get any allies for this fight. Get his health down low enough and he'll start using his Heartless Angel special, which will drop you to 1 HP and 0 MP in an instant. Then if you keep going, he'll pull out even more attacks, including a rain of meteors. It takes a very fine balance and absolute mastery of KH's combat system to take him out, and it'll take a while too, since he has so much health there aren't enough health bar colors to cover it all.

Oh look, it's another one that came back for the sequel! Yep, he also appears in Kingdom Hearts II, and while he's been buffed up in some ways, the change in the combat systems between games makes him a little easier. Granted, only a little. Pretty much everything from the prior fight is still there, except now you can properly see he has 14 health bars.
6. Soul of Sectonia (Kirby Triple Deluxe)

I had to include a Kirby boss in here, didn't I? This boss comes at the very end of the True Arena, a run through of every boss in the game in powered-up forms. Just reaching her is hard enough, much less actually beating her. She starts off as a harder version of Queen Sectonia's final form, using most of the same attacks but in much more difficult to avoid patterns. Once you beat her, though...

Even as just a head, she's still determined to kill Kirby. This phase has no equivalent anywhere else in the game, meaning there's no easy way to learn her patterns. She has the traditional Kirby final boss teleport spam, plus attacks based on Marx Soul, Magolor Soul, and Drawcia Soul, true final bosses from other Kirby games. She doesn't have that much HP, but with how quick she is and how much she teleports around, landing a hit on her is quite an accomplishment.
5. Death Egg Robot (Sonic 2)

This mech built in Dr. Eggman's image is the final boss of Sonic 2. It doesn't look like much, but it's quite dangerous. There are no rings in the entire stage, meaning there's absolutely no room for error here. One hit, and you're dead, and when you die you'll have to defeat the doppelganger Silver Sonic again before you get to face off against this guy. It'll jump around the room and launch its arms as projectiles at you, and it takes 12 hits to defeat, rather than the typical 8 for Sonic bosses.

It returns with a vengeance in Sonic 4: Episode 1. This time you get rings, allowing you to take a few hits, but this becomes a huge endurance fight as it now takes twice as many hits to defeat, and can shield its weak point with a field of electricity, forcing you to throw its arm back at it to damage it. To make things worse, your rings bounce further and further away with each successive hit you take. Even if you do manage to get it down to its last hit point, it'll try to bring the entire station down with it, so you'd better deliver that final blow quickly.
4. Sans (Undertale)

You feel like you're going to have a bad time.
Anyone who's played or heard anything about Undertale will know it would be a damn shame if I left this memorable fight out. Normally Sans is a goofy, friendly skeleton who sits around doing nothing all day, but if you go on a genocide path and kill absolutely everything, he gets serious. He dies in one hit and his attacks only deal 1 damage, but with no invincibility frames and a damage over time effect, he can reduce you to 1 HP and kill you off in a matter of seconds. To top it off, he'll also break the fourth wall to avoid all your attacks, and attack you while you're on the menu. He knows you come back after each time you're killed, so he's really just trying to get you to give up, and I know several people who did indeed give up after this nightmare of a battle.
3. Lord Brevon (Freedom Planet)

Even in a game where 90% of the difficulty is from the bosses, Brevon manages to stand head and shoulders above them all. He's so fast it's hard to keep him on the screen, and his poison-coated knife can take off half your health in an instant. He can also throw you, and is equipped with got mines, a laser gun, and a teleportation field that causes damage if you're caught in it. His only saving grace is that he has a predictable pattern, and you'll have to learn it by heart and not miss a step if you ever want to defeat him. On the hardest difficulty, he doesn't even have that.
Past this point are bosses that I haven't even manged to beat.
2. Gurglewocky (Giana Sisters: Twisted Dreams)

Look at how smug this guy looks. You can't do a thing to him, and he knows it. This T. Rex-like dragon is the final boss of Giana Sisters: Twisted Dreams, and a graduate of the Mario-style school of bosses that you have to defeat by using their own attacks against them. He'll attack with fireballs and burning breath which is red for Cute Giana, blue for Punk Giana, and equally lethal for both. Figuring out how to hurt him is enough of a challenge in itself: You first need to get him to spit out a fiery boulder (which will chase you), then hit it with his fire breath of the opposite color. After the first hit, he'll light the floor on fire too. It's a downright brutal endurance match that requires all your best dodging and platforming skills, and that's probably why I haven't beaten it yet.
1. Ozma (Final Fantasy IX)

This sphere-shaped thing is really just one of the, if not the, most brutal bonus bosses I've ever encountered. Oh, sure, it doesn't have anything super flashy, and it only has 65536 HP instead of the typical millions for RPG bosses, but it's still an outright painful encounter that has ended in failure every single time. Ozma just keeps nuking you over and over with all kinds of high level magic, and there is just no way to make it stop. It floats out of range of melee attacks, and it absorbs Shadow elemental damage, preventing you from using Vivi and Dagger's best spell and summon respectively. However it's perfectly happy to use Vivi's Doomsday spell on you, dealing incredible damage and healing itself along the way. Even if you have gear to protect against Shadow, that still won't save you since it's also got a ton of other high level spells like Flare, Meteor, Holy, and more, plus Curse, an attack that deals high damage and can cause pretty much every negative status in the game. Another boss could use this move on a 5-turn countdown, while Ozma can just pull it off whenever it feels like. Speaking of which, it also gets an extra turn each time your characters take a turn! Good luck trying to do anything with that around. If you help all the friendly monsters, it's made slightly easier by allowing it to be hit in melee and removing its Shadow absorb, but even with that, this is a ridiculous fight that even a level 99 party can fall against in one cast of Meteor.
And there you have it: 10 bosses who can each make you scream for mercy. An honorable mention goes to Absolute Virtue from Final Fantasy XI, which I've never tried to fight seriously, but basically dominated the endgame scene for a time due to being virtually undefeatable.