To me, the best heel run was Bret Hart's run in 1997. Though it only lasted 8 months, the Hart heel run had a brilliant beginning, middle and end unlike any other heel run in wrestling history.
The Beginning: One of the greatest WrestleMania matches of all time, Hart entered the match as a baby face and was converted to the hated villain halfway through the bout. This match not only made Hart the top heel in the company, but it really pushed Steve Austin over the top as a bonafide STAR. While KOTR put Austin on the map with the WWE crowd, his feud with Hart put him at the top of the company ... and the match at WrestleMania 13 solidified him as the most "over" star in the company.
The End: The heel run ended with the most controversial moment in the history of the WWE, the Montreal Screw Job. Indirectly, this match created the Mr. McMahon character -- thus, one could say that Bret Hart "put over" both Steve Austin and Mr. McMahon, the two driving forces in the WWE reclaiming the top spot in the war against WCW. How many heel runs can claim that they "made" TWO of the most iconic wrestling figures of all time?
In between "making" Austin and Mr. McMahon, Hart gave us the meat of one of the greatest rivalries in WWE history. Though they had wrestled against one another in tag team matches, mid-card matches, and even headlined a WrestleMania, 1997 provided us the first - and only - time Hart and Michaels really went after each other as bonafide main event stars. The personal feud between the two not only provided a precursor to The Attitude Era, but it also shifted Raw from a cartoonish product into a more realistic product... which was a necessary move in order to compete with Nitro's more realistic approach.
To me, there's no heel run in wrestling history that provided the entertainment and history that Hart's run did. Though it only lasted 8 months, one could argue that the brevity of the run was perfect in that it didn't get old or stale. For me, there was no point during Hart's heel run where I said to myself, "Will they end this already?" ... and honestly, after about 2 years, I had that exact thought with Triple H, Hogan and Mr. McMahon. Those runs ran so long that ideas were being recycled after a while.