What a tricky question. I loved the entire final battle sequence. I think it is possibly one of the more epic boss fights I've played. When that chalice revealed itself to actually be useful to the story after all that time might have been my first memory of that "tingly" feeling I get when something epic happens.
But then the Stained Glass Demon has a fantastic design to it, (PS1 original of course), back when I was younger and I played it I think I found that the most scariest of the boss fights because of how in-human it was, the loud noise it makes when breaking free, and the first time you hear the most nerve-wrecking soundtrack ever to grace a boss battle.
"Bugger! Right then, that's it! I've had just about enough of your meddling! Where's that spell." - Zarok
I think it's got to be the stain glass demon .because one he's an awesome boss and also he's sometimes quite a challenge to beat if you don't get your weapons stolen by the gremlins ( I don't know if there ed gremlins I've forgotten what they are called).
Oh yeah forgot that, but what a boss the stain glass demon. Only one company could of designed that and it was Sce Cambridge aka guerrilla. But I also admit I love defeating zarok and lord kardok aswell.