I have to go with the Hitman, Bret Hart. He pretty much carried the WWE for most of the 90's, during a time when the WWF was struggling, and it's reputation hurt by the steroid scandal of the early 90's. Even when Bret wasn't the champion, he was usually heavily featured, and more than once was asked to do multiple matches on PPV. Not to mention, he was so instrumental in getting several of the other guys on this list over. He helped to make Shawn Michaels a true main eventer, with their epic Iron man match. Stone Cold Steve Austin really began to get over when he started to feud with Bret. Razor Ramon even had a short feud with the Hitman, fighting him for the WWF title at the Royal Rumble in 93.
Here is why I think Bret wins out over some of the others:
Sting - I just always felt the surfer gimmick that Sting had for most of the 90's was just so generic. And when he became the crow gimmick, I liked it, but the fact is he didnt wrestle for almost a year, so really his prime time was only from 98 and on in my opinion, and two years isnt enough time on top to be the wrestler of the decade.
Hogan - I never really cared for Hogan up until the formation of the nWo, like Sting I felt the red and yellow was to generic. Plus, in ring, Hogan definately started slipping through the 90's, and by the time of the nWo, it seemed like his move set was pretty basic, cheap heel stuff.
Flair - Again, just not as good in the 90's as he was in the 80's. While still as entertaining as ever on the mic, his matches throughout the 90's became slower and shorter, and more predictable.
Undertaker - Probably the hardest to argue against, but he really spent a large part of the 90's in the mid-card. He came in strong, had a very brief title reign, then from 92 to 97, dropped back down to mid-card, fighting in a lot of pointless, forgettable feuds. Plus, in the ring, while the Undertaker was never bad by any means, I feel he didn't really start to hit his stride until 96/97, when they started to loosen up on the more gimmicky aspects of his character.
Shawn Michaels - again, hard to argue against, but like Taker, he spent most of his time in the mid-card. Plus Michaels was well known for his attitude problems in the 90s, and really only had 2 solid years on top (96-98), before retiring for the first time. Not to mention he almost never dropped a belt to anyone, forfeiting most of his titles instead of loosing them.
Stone Cold - again spent most of the 90's in the mid-card, he jumped for WCW to ECW to WWF, getting stuck with the ringmaster gimmick for the first part of his WWF career. And like many of the others, really only had a couple years on top.
Most of others I feel are pretty obvious, so I wont go into detail, but Bret, IMO, was truly THE wrestler of the 90's, having classic feuds with the likes of Mr. Perfect and Roddy Piper over the IC title, his rise to the main event beating Ric Flair for the WWF title (which he would hold a total of 5 times throughout the 90s, which at the time, I believe tied Hogan for most reigns ever), to the King of the Ring, the PWI #1 on the top 500 list for both 93 and 94, to his feuds with Michaels and Austin. And even his run in WCW, while not as good as it should have been, he still was a multi-time US Champ, a Tag-Champ, and a 2 time WCW World Champion.
(Didnt mean to go on for so long, but before anyone decides they want to go through my arguments and dissect them and debate them, feel free to argue why you disagree but I dont plan on coming back here and arguing every little fact, I am just stating my opinion, you are more than welcome to do the same)