I've had several like this. Let's go through them:
Everyone's mentioned RAAM, so I think I'll just mention him and be done.
One who deserves special mention here is Nebilhim from Tales of the Abyss. First of all, she's level 100 (quick note: the final boss is in the 60s, which is the level cap for all enemies outside the colosseum), and has almost full stats for everything, meaning All-Divide (rare item that halves damage done by both enemies and allies. They're only useful on bonus fights) or die. In addition, she has a rare, one of a kind item you have to steal early on, or you'll never see it again, though you can only steal if before battle you equiped an item to a skill. Plus, there's only a 25% chance you'll get it if you attempt to steal. As for her attacks, she has every high powered spell in the game, AND she can freeze time later on. You can only carry 16 of each item, meaning you only have 16 nonspell revives. After finally defeating her, I went to claim my reward, only to find out that to get the Title for beating her, you had to do it on a harder difficulty. That's right, the bonus boss was laughing at me from beyond the grave.
Another Tales Bonus Boss dealing with collecting cursed weapons is even worse. Let's look at Vesperia, where if you decided to collect the cursed weapons because you love sidequests, you're in for a nasty surprise. Turns out, the final boss gets another form, on that is several levels past his previous one. This wouldn't be as bad, if there were any mention of this happening before hand (hell, even the strategy guide won't warn you about it).
Dead Rising was mentioned here several times, but I never saw the convicts on it. Not only do they appear after your first boss battle, but it will likely be night time then (meaning super zombies). They have three attacks, four health bars, and at this point in the game you're probably not going to be equiped for them. Also, they're between you and near suicidal survivor, meaning 100%ists are gonna be pissed.
However, I'd like to point out that back in the days of the NES, a lot of bosses were like this. In fact, some were so hard, they made the game multiplayer. For example, with Megaman we did this when I was a kid: you played through not to win the level, but to get further than the last player. If you got to the boss, the amount of life left was what mattered. If you were able to beat him, the entire room let out an applause (though no one would write down the code since you had no more lives more often than not).