How about the Dark Water level from Ecco the Dolphin?
http://www.youtube.com/watch?v=hejfMH4r41c(starts at 2:07)
The boss is actually much harder than the player made it seem. You have to hit 4 of the same color globes without getting killed. Mind you:
- Hitting a globe of another color resets it.
- Waiting in place for longer than say.... a second will prompt an attack that kills you in 2 hits if you are at full health.
- While you're swimming up and down trying to time your attack right, your air will run out and you will drown.
Getting to the level requires password input that the video shows (under the title "Dark Water") and it's a sega genisis/ megadrive game.
Ecco has some other nasty levels without bosses.... I just thought this would be the most frustrating.