Dark Souls, Anor Londo. I had ascended my Flame, and the Great Combustion Pyromancy, I discovered, tore through the Silver Knights and Elite Giants with ease. I was thinking that I had finally hit my stride...
And then THEY showed up. Ornstein and Smough.
I have no idea how many times I died to that insane duo, they slaughtered me and sent me packing every time. Even with the aid of the wondrous Solaire, those two would serve me up on a silver platter every time. The worst was getting to Super-Ornstein, because I knew that this would not end well.
I eventually killed SO, but only because of aid from multiple Phantoms.
I have yet to beat them on my own.
Another I'd like to mention is Metroid Fusion, although it was probably because of the fear for one of them.
The first instance for me was Nightmare, I was able to deal with those swimming Space Pirates, no problem. The ugly fish? Please. Then I came across Nightmare, and it was a pretty bad dream. Missiles made useless in the beginning, then he just got worse as it went on.
Then of course came the part where I was running for my life from SA-X, where I must have died at least four times in the first area, and countless other times along the way. It wasn't even a boss, I was just trying to escape.