"You and Me and Pokemon" has every single Pokemon the show made come out to dance with the human cast. The lyrics are heartwarming as well, talking about the bonds people have with Pokemon.
Team Rocket complimenting the audience on saying "TEAM ROCKET!" loudly.
Ash, Misty, and Brock singing "My Best Friends."
Professor Oak and Delia's actors were dating at the time of the show, and this is referenced in-show by Ship Teasing them.
"Everything Changes" has Professor Oak helping Delia come to terms with the fact that Ash is growing up.
Professor Oak: ...Boys become young men, whether or not they're Pokemon trainers!
"Misty's Song" is even sweeter/sadder than the 2BA Master version.
Meowth helping Jessie and James feel better by saying they're the best at being the worst.
Brock seeing that Misty loves Ash, despite her denial.
Mewtwo defeating MechaMew2 by teaching it compassion, courtesy of Ash and his memories/pure heart.
MechaMew2's speech just before blowing itself up.
Giovanni: I didn't give you the power of speech! MechaMew2: You didn't give me a lot of things, but you did give me the ability to learn. And I have. From the boy, I've learned about love and goodness. His heart is pure. His love for Pokemon and his friends and family is real. I've learned right from wrong, and I've learned which one you are. Now I know what I must do. Something else I learned... Self Destruct.
Before blowing up, MechaMew2 tells Mewtwo to take an unconscious Ash to where he'll be safe.
Ash's talk with his mom in the last scene.
In the Finale, Giovanni comes out with smudges all over his face and suit and glares at the cast, until the heroes invite him to dance. Albeit reluctantly, he does.
The Finale has every member of the cast dancing with all the Pokemon, including Team Rocket.