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..