Hardest RPG boss ever: Malroth from Dragon Warrior 2. He didn't have any cheap one-hit kill attacks like some bosses, but he did enough damage to keep your healer occupied (or worse), had enough HP to withstand several rounds of fighting, and.. CAST HEALALL LIKE IT WAS GOING OUT OF STYLE! Even at maximum level, you stood a fairly good chance of not being able to kill him (so much for the "all you have to do is level up" theory).
On that note, I'd like to nominate the entire game as exceptionally cruel.
Runners up: Chaos (FF1) and Lavos (Chrono Trigger) were hard if you fought them at the level where you would normally reach them, without doing any level-building on the side.. more so than many RPG bosses, I'd say.
Honorable mention: The Dragonlord, Dragon Warrior 1.. at level 16. One level before you get Healmore. Yes, that means you're fighting him with HERBS. Can you do it? I never could, but I'm convinced it's possible.
Anyone who has trouble with bosses in FF games from the second half of the series is a pussy. I'm sorry, the truth may hurt but it had to be said.
Hardest action boss: Who the hell knows? There are literally thousands of these games and many of them have insanely hard end bosses, especially when they started in the arcade ("insert one credit to continue.. 10.. 9.. 8..."). With that said...
The Grim Reaper from Castlevania was the horror of my young gaming days. In my mind, I will always imagine his room as containing great heaps of rotting Belmonts in the background, even if I did finally beat him sometime last year.
Nearly anything on higher difficulty levels of Devil May Cry. If you haven't played this game, or you only rented it and played it on Easy, give the real thing a shot. It will scar your soft, pink flesh with cruel metal whips and fire and send you home, broken and crying for God and Mommy.
The ultimate end boss in Demon's Crest is hard, certainly, but not insanely hard; once you get a feel for how he fights (it's a very simple pattern) you should be able to spank him handily if you're smart enough to use the right items at the right times. I forget how the ending goes, though.. Doesn't Firebrand get the Super Übercrest of Infinite Hurting and go on to conquer the world, or something? Dammit, the world needs another game like that.. good gameplay, awesome dark pseudogothic atmosphere.