There are only 2 Hell in a Cell matches which would qualify as something special - the very first one between the Undertaker and Shawn Michaels at Badd Blood 1997, and the infamous Undertaker vs Mankind match at King Of The Ring 1998. Anyone who feels that some other Hell in a Cell match was better has something wrong with his/ her estimation of brutality, wrestling skill and story-telling.
The Undertaker vs Mankind Hell in a Cell match is widely considered to be the greatest of all time because of the memorable moments which it had, that are imprinted in the minds of wrestling fans. Nobody can forget the moment when Undertaker threw Mankind from the top of the cell to the Spanish announce desk 25 feet below (which is the most TV-played moment in pro-wrestling history), and the fact that Mankind was still able to come back and climb to the top of the cage again. They call Stone Cold Steve Austin the toughest S.O.B. but that's such a big joke - in reality, there was nobody tougher than Mankind. Then the choke-slam to Mankind on the top of the cell which resulted in the cell's roof getting broken due to the impact with Mankind falling 20 feet below on the ring with a chair knocking his teeth, rendering him unconscious for a few minutes. I don't think there has been any other moment when a wrestler has actually been knocked unconscious during a match and the doctor has rushed to the ring before the match got over. To add to it, the fact that Mankind was body-slammed and again choke-slammed on a mat full of thousands of board-pins (thumb-tacks) really made this match the most memorable match ever. Anybody who had seen this match would never forget it and it would stand out in their memory (that goes double for those who attended it in person), because they will never get to see a match like that again.
You have to give credit to the Undertaker for his presence of mind in the match. Despite being very good friends with Mankind in reality, his professionalism didn't allow him to break his on-screen death-oriented character although he was concerned about Mankind's situation. During the first fall, he thought that he has ended Mankind's career and during the second fall, he thought that he has killed him. However, in both the cases, Undertaker just kept looking down at Mankind without showing any emotion (neither joy nor sorrow) though he was very concerned about Mankind's situation. He was competing in the match with a legitimately broken leg and yet he made a jump from the top of the cell to the mat below when Mankind accidentally broke the roof during that choke-slam. You could tell that it wasn't planned for the roof to break (though some people say it was) because they wouldn't have planned for Undertaker to jump from the roof to the ring below with a broken leg. The Undertaker then spent time beating Terry Funk inside the ring, looking at Mankind all the time, giving him time to get up - that is how the Undertaker can handle situations on-the-fly in the ring while maintaining his character, when things go wrong. He then also allowed Mankind to give him a beating and rammed his own head against the steel of the cell, making the match look double-sided. Although, you knew when he kicked out of the Mandible Claw, that the Undertaker will win.
All in all, this was a very perfectly executed match with the most brutality you'd ever get to see and the best presence of mind from the Undertaker in handling the accidents, yet not breaking his kayfabe gimmick. Some call it the match of the year, some call it the best cell match of all time, some call it the greatest match of all time. It was a perfect culmination of a very long and personal on-screen rivalry, whose seeds had been laid when Undertaker's long-time friend Paul Bearer had betrayed him for Mankind. In my estimation, the Undertaker vs Mankind rivalry gave us the best and the most brutal matches, and they showed us something that we had never seen before and something that we will never see again - that is why it will remain the greatest rivalry of all time for me.
Now let's discuss the Undertaker vs Shawn Michaels - the very first Hell in a Cell match. As far as I remember, this was the first time that these 2 were in the ring in a singles' match, and they performed at such a stupendous level that it happens to be the only Hell in a Cell match which received a 5-star rating from Wrestling Observer Newsletter's editor Dave Meltzer. After that, Dave has never given a 5-star rating to any WWE match, which tells you how great this match was.
This was the first Hell in a Cell match, so it scores higher in "innovation" than the Hell in a Cell with Mankind. The rivalry between the Undertaker and Shawn Michaels had reached such a bitter stage (due to Shawn hitting Undertaker multiple times with a steel chair and even costing him his title-loss to Bret Hart), that a steel cage or a casket match were not enough to seal it. So the Undertaker wanted Michaels in a cell from which he could not escape. The match started with Shawn entering the cell and looking scared, and Undertaker making his fabulous entrance intimidating not only Shawn but everyone in the arena and those watching on TV (and I mean it). You didn't know what to expect, because the Undertaker had until then been the most dominant and destructive superstar in the WWE ever, and if you make him angry it is sure going to be hell for you. Shawn took a beating like I have never seen before, but still managed to fight back. In fact, during the time when he gave a reverse piledriver to the Undertaker on the steel steps, I actually thought that Undertaker might lose the match cleanly. If they could make the match look so double-sided, what else do you want? The moments when they brawled at the top of the ring, when they brawled outside the ring and Undertaker rammed Michaels' head into the steel, and when he threw Michaels from the middle of the cell's wall to the announce-desk were acts of violence that we had never seen before in wrestling before. They gave you an idea of what was going to come in the Undertaker vs Mankind match.
Finally, when the Undertaker gave Michaels a thunderous choke-slam from the turn-buckle and signalled for the tombstone. This is when Kane entered with Paul Bearer and the Undertaker just looked on with a surprise. He did not want to fight his own flesh and blood, therefore he just took a tombstone piledriver from Kane on himself. Then Kane put Michaels' hand on the Undertaker, and Michaels won!? Effectively, when the Undertaker signalled for the tombstone by slashing the cut-throat sign, he was signalling that for himself and not for Michaels. That is impeccable story-telling. My God, that was one of the biggest shockers and heart-breakers for me ever. I had got so sick of Undertaker getting screwed again and again in his matches (and that happens even now) that I couldn't bear it. The fans were cheering for the Undertaker with their chants of "Rest in Peace" throughout the match, and everybody was so happy and certain that Undertaker will win when he delivered that Earth-shattering choke-slam. And Kane's interference got him and Michaels the biggest boos ever. But think of the rivalry it created after that between Undertaker and Kane - one of the most memorable of all time. Think of the matches it created like the Inferno match and their first Wrestlemania match. Think of the destructive career that Kane had after that, and what a star-rise he got after it. Finally Glen Jacobs (after playing the roles of Isaac Yankem DDS and the fake Diesel) had received recognition as a character which was the Undertaker's half-brother (so it had to get noticed) and he debuted with such a huge impact that he has since then never looked back at re-creating his gimmick. That was genius!
The fact that despite being the better man and giving Michaels a beating of a life-time, the Undertaker still lost, showed us what the possibilities are in a Hell in a Cell and that you can never be sure of the outcome. The story-telling in this match with the debut of Kane was phenomenal. This match was not about just 2 or 3 BIG bumps where you thought that you already knew the outcome of the match, but it was a more gradual progression from one opponent towards beating the hell out of the other (as bad as had never been seen before) and still losing. The Undertaker himself says that this is his favourite match of all time though he lost it, and "that" coming from the words of the most experienced and respected wrestler in the WWE ring means something. He has stood in the squared-circle against everyone, superstars of all sizes and skill. If he calls a match his best, it damn right has to be. From a story-telling, innovation and wrestling-skill-display perspective (as well as figuring out the result), this match has got to be better.
If I have to recommend a match to somebody for watching, I would still recommend Undertaker vs Mankind before I recommend Undertaker vs Shawn Michaels. I personally liked Undertaker vs Mankind more, and it might be my favourite match but I think that the Undertaker vs Shawn Michaels Hell in a Cell was, overall, the better match.

