Perhaps "Blackout" is the most triumphant example.
Also Camila's solo, "Enough".
Both Piragua and the Reprise.
Definitely "Blackout". The audience goes crazy when we get a glimpse of the cast stumbling about in the dark. Also "96,000", it's probably the show's most famous number, if you don't know why, go find out!
Sonny and Graffiti Pete's section of "Blackout", in which they protect the bodega and distract the vandals. We also see Pete "light" a firework, which looks very realistic. It's also all shades of FREAKING AWESOME.
At the beginning of Act 2, a vest-clad Benny is seen standing on his fire escape. When a T-shirt clad (translation: post-coital) Nina comes out to join him, the audience applauded and cheered for so long, the actors had to start their dialogue over.
Nina: Are you ready to try again, Benny: I think I'm ready", ...and then she starts to test Benny on Spanish vocab words.
Lin-Miranda Manuel's Tony acceptance speech for Best Score. Complete with improvised rapping.
I don't know about God but I believe in Chris Jackson!"
Towards the end of the play, Sonny hires Graffiti Pete to paint a mural of Abuela Claudia on the graffiti-defaced corner store grate. The mural convinces Usnavi, who disliked Pete before, to stay in Washington Heights.
Benny standing up to Kevin after being harassed for not being Latino through out the whole play and being fired deserves a mention.
Camila's solo "Enough," in which she tells Nina and Kevin that they both messed up royally, and that they better fix it.