Let's see... Tone breakingly hard bosses huh? well a lot of the ones I'm about to say might not be like that, but they are some ones that pissed me the hell off.
First up is Deviljho. O. My. . Just wandering around the elite ranked quests, Hunting down a peco. O how cute he summoned another monster. What's it gonna be Rathian? Jaggi? I'm sure it won't be to-whaHOLYCRAPWTFISTHAT I've never seen one of those before! I wonder how O sweet crap on a pop stick did that fucker just take out 80% of my health with one attack!
The Deviljho changes the tone of Monster hunter when you get into the high ranks. It's not enough to be able to escape him, you've got to deal with him being in your way. And he is REALLY strong. You don't get a quest to fight him till you've basically beaten the game. I enjoyed the change, found things more exciting, but this guy is at the top of my list of game changing bosses.
Dr. Wily. This guy is un-fucking believable. It's not until Megaman 4 that he really starts becoming a huge pain in the ass, with the wily capsule, but it's a trend that sticks around. That last encounter with Wily tends to be one of the most hair pulling, teeth grinding, wall punching encounters in the game... O yeah and special props to the Yellow Devil. I didn't have a problem with him, but any badguy who makes retro gamers piss themselves has to be mentioned.
I'ma just do one huge blanket one with All the Disgaea secret bosses. These guys usually out level you by a ton. 400-4000 is the general pecking order. These guys are seriously a huge wall to climb.
Zeromus from Final Fantasy 4. If I have to put one RPG on a list, this one is it. He's watered down in a few versions, but if you play either the original Japanese version, or the DS remake, this guy is unfairly powerful. Doesn't use a lot of tricks, he does have one or two, but his big thing is he will nuke the FUCK out of you. That's basically all he does is blow you up!
And now from my own personal hole of misery and pain we have Megaman Juno, from Megaman Legends. I don't know why this guy fucks me over so hard, but FUCK this guy fucks me over... HARD. Even when I know his attacks and how to avoid them, he still takes multiple attempts for me to beat. Even tho I've fought the CRAP out of him, and can beat the entire game barely taking a scratch... Why this guy? It doesn't make sense. Someone help me feel better about this by saying that Juno kicked your ass too! T.T
And lastly... Malroth from the original Dragon warrior 2. He can kill you in 1 hit. He can heal himself back to full health. He can get multiple attacks a round. He will fucking DECIMATE you, even if you are at the max level the game will allow he can still destroy you!