So who or what do you think is the best Villain/Antagonist/Boss in a videogame? Please list your reasons as to why do you think he/she/it is the best. Was it because of the fight, the plot, the story? What is it that is so great? Oh, and, try to avoid spoilers.
Jon Irenicus - Baldur's Gate 2: Shadows of Amn
My all time #1 favorite. The actual fight with Irenicus is not that special or different from any of the other big fights in the game. However, it is the story and plot behind him that really make Irenicus shine. The guy's ambition as well as the way he screws you and Imoen over from the very begining just makes you hate his guts. When you learn his backstory, his reasons as to why he did what he did, one starts to feel a bit sorry for him. However, the sense of satisfaction when I finally killed that bastard was inmense. There is no other villan that I know of that really made me want to be there for real so I could see his body torn asunder.
Yellow 13 and the Aquila (aka Yellow) Squadron - Ace Combat 4
When you finally get to fight them for real, just you against their five plane formation it is the most amazing and challenging fight in the entire game. However what trully makes them shine is the story, it shows you that those you fight are real human beings. That fight really gives you a real sense of accomplishment at emerging victorious, as well as feelings of compassion for those pilots that you shot down.
For some reason I can't think of any others at the moment. If any others come to mind I'll will post them.