I don't know if it'll count, but I'd have to nominate the Battle Arena from Castlevania: Circle of the moon. All thoes rooms filled with monsters who didn't drop anything, with no magic at your disposal, and the devil waiting for you at the end. That section was just freaking insane. If it wasn't for the treasure at the end I wouldn't have wasted all the effort.
Another Mention would have to be the Mobile Armors in Gundam Battle Assault 2.
Tidal Wave from the PS2 Transformers game was the first boss battle I fought that felt impossible without being cheap. As in "how the hell am I supposed to beat THAT thing?" I still think that's the most slept on level possibly in game history. I mean, you play through the dude's BODY as the level and afterwards the ENTIRE LEVEL transforms and you fight it. This was before God of War and Shadow of the Colossus. And it was hard as HELL.
Hells yeah. Basically having to snipe his head, whittling down his HP while running in between two mounds and hoping he doesn't crush you. What made it even more 'fun' was in when you rose the level of difficulty more of thoes annoying Air drones would show up to snipe you. you know, the ones who you needed the Flak Minicon to actually kill with one hit.