I can think of about four bosses that make me ragequit by their sheer cheapness, but the worst two are:
The bonus boss of Golden Sun, Deadbeard, was a pain, but his successor, Dullahan, is cheap as hell. He'll debuff your entire party and the next turn (which, because you're debuffed and he's so fast, will be immediately after) he'll waste you with the second most powerful summon in the game.
The Omega Metroid at the end of Metroid Fusion. You're fighting it in the narrow docking bay, there's no room to dodge and it's claws have ridiculous reach. Any time I've cleared this boss, it's been by sheer luck and dogged determination
"Aras ∂a bi ronde rof oretta,
heard under helme, hiori-sercean bær
under stan-cleofu strengo getruwode
anes mannes; ne bi∂ swylc earges si∂!"
Trusting a 'loth is a lot like keeping a snake for a pet. It's not a matter of 'if' you're going to be bitten, but a matter of 'when'.