Alastair Reynolds is very good at creating villains, although I disagree about you picking Inhibitors. They are too much an impersonal force -- Berserkers with even less individuality.

But almost every character from Reynld's "Chasm City" has various degrees of villainy, and most of them are COOL. Especially the protagonist.

Actually, now that I think of it, Jack Tanner/Cahuella/Sky Haussmann probably IS the greatest (human) villain in science fiction. Of course, he cheats by having three very different personalities. For those who had not read "Chasm City" and the rest of Inhibitors series: Cahuella is an utterly self-centered, flamboyant, almost theatrical crime lord with a passion for hunting. Part Tony Soprano, part Jack Sparrow. Sky Haussmann is truly creepy -- brilliant, charismatic, and incredibly patient sadist and psychopath. Hannibal Lechter with political power. And Jack Tanner is not really a villain -- a very cold-blooded, but honorable soldier with almost supernatural combat skills. Brooding, and driven by what he knows is a hopeless vendetta. Part James Bond, part Elric of Melnibone.

And if you want to include utterly inhuman aliens among "best antagonist", I think you can't do better than MorningLightMountain in Peter Hamilton's "Pandora's Star" and its sequel. A hive intelligence similar to Borg or Inhibitors, but far better fleshed out. Hamilton managed to do what I really thought to be impossible -- presented the viewpoint of an intelligence so different as to find humans incomprehensible, and made the reader understand that viewpoint. Which makes MorningLightMountain even more terrifying.

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Fiction has to be plausible. Reality is under no such constraint.