Roy Batty got my first Choice, Blackie DuQuesne.
Yama, against Sam, in 'Lord of Light'. I like him because he goes from antagonist to ally.
The Borshin, also from Zelazny, in 'Jack of Shadows'. Really creepy.
Stretch, the computer in Bester's 'Indian Giver'
Lincoln Powell, the esper cop who tries to nail Ben Reich in 'The Demolished Man'
And must mention Gulliver Foyle from 'The Stars My Destination', who was arguably his own antagonist.