There's an Austin v Angle match that was Smackdown that was pretty great too. It was right near Austin retiring.
I'd say the three most important matches of that era were Shawn Michaels/Undertaker in the first ever Hell In A Cell at Bad Blood which was basically the match that really ushered in the era, Stone Cold Steve Austin/The Undertaker in their First Blood match at Fully Loaded which was personified the whole era and Austin/McMahon and then Stone Cold Steve Austin/The Rock at WrestleMania 17 which was the peak and biggest match of the era.
If i had to choose the best three matches of that era instead of the biggest or most important then i would still go with Shawn Michaels/Undertaker in the first ever Hell In A Cell at Bad Blood as in my opinion it's still the best match that match concept has ever seen and is still HUGELY entertaining to watch now fifteen years later. I would then go with Stone Cold Steve Austin/Triple H in their Three Stages Of Hell match at No Way Out which was the start of an epic series of matches that year for Stone Cold Steve Austin and is arguably the best match of each mans career. The final choice would be a straight fight between TLC 1 or TLC 2 with Edge and Christian, The Hardys and The Dudleys at Summerslam 2000 and WrestleMania 17 but i'm hard pushed to choose between them so i'll cheat and throw them both in as a tie.