Some of my favorites (not necessarily best, just ones I really enjoy):
Dreamgirls - Jennifer Holliday; you can't not love this performance!
Anything Goes - Sutton Foster; was never a fan of Sutton before this, but she is absolutely BEAMING in this performance and her dancing is spectacular.
42nd Street - 2001 revival I'm a sucker for those pre-taped performances, especially if they involve the subway
A Chorus Line - OBC; no explanation required.
Fun Home - This performance instantly made me book a trip to NY and buy tickets to the show. Sadly, I ended up thinking the show suffered of severe over-hype (not the show's fault), but this number did everything a Tony performance should do
Next to Normal - Alice Ripley is pure fire in this performance
Ragtime - OBC I get chills everytime the triangle formation begins, also special shout out to Christiane Noll's performance that was terribly mistreated and cutoff at the 2010 Tony's.
If/Then - Performance did a beautifu job of showing how much emotion and power you can convey without a ridiculous amount of glitz and setpieces.
Some I thought fizzled and died: Xanadu, aside from Cheyenne Jackson in those shorts, it did nothing to make me want to see this show, have seen it since and enjoyed but I don't think that was the right song/moment to highlight for the show. Legally Blonde, enough has been said about this performance. Cabaret, most recent revival of the revival just made Alan's performance of Willkommen tired and boring, the song had already been performed TWICE at the Tony's. It's beyond me why they didn't chose to highlight a different song.