Ok..
The final boss, or should I say final "bosses" from Eternal Darkness was kinda hard. It was, to me, one of the nicest recent boss level I played.
I know somebody already mentioned this but yeah, Sonic Adventure 2 Biolizard boss was pretty tough too [nice music on that level btw].
This isn't a boss level but I thought I would never get past the Fear Test on Starfox Adventures! Plus, I was kinda disappointed with the final boss on that game.. Tres easy final boss I thought..but it was still a cool game.
Has anybody ever played Sword of the Berserk for Dreamcast? The FIRST stupid boss that looked like a bull?! Gawd, my fingers had blisters from that one! I thought it was pretty hard for the FIRST boss...
And I had a tough time on Code Veronica with the Tyrant from the cockpit. It took me a while to evade/shoot it/then push the button for that box thingy to push him off the plane..but I did it one day while I wasn't trying too hard and succeeded..