I suppose it would have to be Triple H. He was the top heel for years in that time frame and he sure was hated.
JBL also comes to mind. His wrestling skills may have been bland, but his character was exceptional. He had a long run as champion, too, and drew a ton of heat.
As does Edge. One of the main stays of the company and something solid they could always fall back on. He carried the Smackdown brand for a long time. His longevity on top actually puts him before JBL.
Honorable mention #1: Chris Jericho. After he reinvented himself and started feuding with Shawn Michaels, for a time what they had was magic. It catapulted Jericho at long last to that level everyone always felt Jericho had in him but never quite reached until then. And then Jericho did the impossible: He and Big Show made the tag team title MEAN SOMETHING. As soon as they dropped the titles they meant nothing again. It was all Jericho. Awesome heel, one of the all time greats.
Honorable mention #2: Vickie Guerrero. I can only imagine that Eddie must be proud of her. The most hated heel in the company. More heat than Michael Cole, more heat than the Miz, more than Punk, Del Rio, Sheamus or Barrett. Not bad for someone who was never meant to be a performer. If she was a dude, she would have been champion multiple times by now.