WrestleMania 2000 was the first time in the history of the WWE that a heel won the main event at WrestleMania (which culminates and, so far as is possible for such an on-going melodrama, finalizes the plotlines of the whole year leading up to it) and didn't immediately lose the title. Furthermore, the heel in question (Triple H) won over THREE OTHER top contenders in the biz (Mick Foley, The Rock, and The Big Show). In fact, Triple H has had long, extended victories over fan favorites as champion time and again, despite frequently being a heel during many of these periods. For example, he once won a "six-pack" championship match over FIVE OTHER opponents, all of whom were either faces at the time, or effectively faces by circumstance of being current enemies of his.
Even when he is in heel mode, The Undertaker never loses at WrestleMania. (As a matter of fact, most of the time he doesn't lose much at all, regardless of whether or not he's a heel.)
A common tradition in professional wrestling has often been to have a new superstar of whom great things are expected get off to a great and usually long unbroken winning streak, and this is at least as common for heels as it is for faces. To cite the Undertaker again, he was a heel for a long time after joining up at the WWE/WWF, yet had a starting undefeated streak for something like his first year-and-a-half during which he beat such legends as Jimmy Snuka and Hulk Hogan. It didn't end until Hogan was able to beat him — only in a rematch and only by cheating. And given that Hogan's own gimmick involved practically never losing, the fact that he needed to cheat just made 'Taker look even stronger.
One laced with Unfortunate Implications from WrestleMania XIX - Triple H was due to defend the World Heavyweight Championship against Booker T. The central arc of the feud centered around the fact that Booker is black - Trips would say things like that people like Booker aren't good enough to be champion and do things like offer to pay Booker to carry his bags, he showed Booker's mugshot from when he was younger and robbed a Wendy's, and things of that nature. In a promo before the match, Trips went for an Author's Saving Throw by saying that when he said all of those things about Booker, he wasn't talking about him being black, but that didn't do much to deter the implications. When the match ultimately came around, Hunter won fairly easily, including waiting about a full minute after hitting his finisher to pin Booker (although that was a result of Triple H botching the finish, resulting in Booker legitimately being injured).
At TNABound For Glory "10.10.10.", Abyss's prophecy of "They" coming to take over TNA came true in the form of "Immortal." Led by Hulk Hogan, who now has complete control of TNA.
Vince McMahon in 2003. While a few of the examples above refer to simply PPVs (e.g. after WrestleMania 2000, the storyline continued, ending with Rock pinning Vince at King of the Ring to win the title), Vince not only won an overall feud in 2003, but all of them. He lost to Hogan at WrestleMania XIX, but ultimately fired Hogan, defeated a one legged wrestler he had a grudge against, manipulated Brock Lesnar into turning against Kurt Angle which led to Lesnar winning the WWE title (and throwing said one legged wrestler down the stairs), beat up his own daughter on PPV which resulted in her losing her job, and later buried The Undertaker alive with help from Kane. The entire year was setting up his comeuppance, but Vince never got his and simply pulled a Heel-Face Turn at WrestleMania XX.
Vince pulled a real life one with the Montreal Screwjob. Vince screwed over a popular longtime wrestler and managed to spin it into a renewed surge of popularity.
Happened at WrestleMania X-7 where Stone Cold Steve Austin turned heel and sided with Vince McMahon in order to beat the Rock for the championship.
(Heel) CM Punk at Money In The Bank 2011 defeats John Cena for the WWE title and leaves the company with it, the way he promised he would. When Alberto Del Rio comes down to try to cash in the briefcase, Punk just kicks him in the head and leaves the building, and the company, through the crowd with the title. Then again, he was massively popular, and the PPV was in his hometown of Chicago, so many were happy with the result anyway.
At King of the Ring 1993, Yokozuna was out for revenge after he lost the WWF Championship at WrestleMania IX to Hulk Hogan the same night he won it. This culminated in a match where Yokozuna won after a photographer (who was actually Harvey Wippleman in disguise) shot a fireball out of his camera at Hogan, allowing Yokozuna to use the atomic leg drop on Hogan for the win. After the match, Yokozuna used the Banzai Drop on Hogan. This turned out to be Hogan's last appearance in the WWF until 2002. "Hulkamania is dead" indeed.
One of the many problems in WCW was that the faces rarely won, especially when the New World Order was involved. In fact, this was cited as one of many, many reasons WCW went under. Fans stopped caring because they figured the heel was going to win anyway.
Dragon Gate is a very factionalized wrestling promotion, with most angles being stable vs stable feuds. And the heel stables almost invariably win these feuds. Generally the heel stable wins the feud and then either the heel stable's leader or second in command breaks up with the stable and starts a new stable. The most recent example (as of October 2013) would be the feud between Mad Blankey (heel) and Akatsuki (face), which ended with Akatsuki losing and then YAMATO usurping leadership of Mad Blankey from Akira Tozawa and kicking him out of the stable.