HBK never had a bad match at WM, but certain matches were historic in terms of their significance to the pro wrestling scene while others (like HBK vs Jericho) were simply great matches, but didn't have the historical impact.
Considering the fact that he was seriously injured (unlike oher times when he was accused of faking injuries to avoid being pinned and losing), HBK's performance vs Austin is probably his best. WWE needed that match to be good and needed Austin to win finally win the title outright or two years of Stone Cold Mania would have been wasted. That match, that WM, really helped spark the WWE comeback after some pretty lean years, much of that time looking up at WCW.
The Flair match had more emotion than anything I've seen probably in the last 15 years. Probably the best match you'll ever see with a 59 yr old combatant, and from start to finish they made you believe the match would possibly end a different way even though every ounce of common sense in the world said it would go down much as it did. When two guys can convince you a match could swing the other way when you know it's almost impoosible, that's showmanship
His last match vs Taker was brutal, and significant in the sense that these are two of the most enduring stars in WWE over the last 15 yrs, also a great challenge to Taker's streak. Again, realistically you knew HBK wouldn't end the streak, but this match was so close you reallylet yourself think holy @#@# he might win this thing!!
Not too many guys can wrestle an Iron Man Match and keep it interesting. In 25 yrs of wrestling, I can think of maybe 6 main event caliber performers who in their prime could do that. This match was also significant because it was HBK's first World Title win, and the beginning of his ascension over Brett Hart as the company's top star (at least until Stone Cold)
The Ladder Match was a turning point because no one was doing Ladder matches, I know that HBK & Hart did one at a non televised show a few yrs earlier (Hart did some Iron Man Matches with Flair at non televised shows in 93 also), but this match helped this format become popular. It's also the first time in HBK's career that he really stole the show at WM, his prior matches all good but not "showstopping" material. Scott Hall was also not a great performer. Having great matches with Hart, Austin, Taker, and Flair is pretty good, having a great match with Hall, who is clearly good but nowhere near great, that is a special accomplishment. Remember, they don't call Flair great because he had great matches with Steamboat, they call him great because he had great matches with guys like Lex Luger, who looked like a million bucks when he faced Flair in 1988, better than he looked against any other opponent.
I would take any one of these, part of me wants to vote for Austin because of the injury, and how big the match was for WWE, part of me wants to vote for Flair because it's probably his most unforgettable match, but I'll vote for the Ladder Match.