This sideways shot of Jack staring down FLocke from a distance as the island is starting to be destroyed:

The fact that the last 5 minutes of the finale had
zero dialog (minus one line from Locke to Jack: "They're all waiting for you").
Ben sitting alone outside the church, even though both Locke and Hurley invite him in...very poignant scene. And Ben's reaction to seeing Hurley walk out of the church--the delight and warmth in his "Hello, Hugo" was incredibly sincere.
Vincent laying down next to Jack at the very end (as others have mentioned)...incredibly sad and beautiful at the same time.
Having the last image Jack will ever see in his life be that he did get the plane off the island afterall.
FLocke bleeding for the first time ever after Jack started punching him...and FLocke's expression on his face when he realized he was now vulnerable.
Every single one of the "breakthroughs" in the ALT...all were very emotional. Well, except the Sayid/Shannon one lol...but even that one had me going "Oh, s**t, it's Shannon" and laughing lol...
The moment I realized Hurley, and not Jack, was going to be the new island protector.
Seeing Rose and Bernard as the ones who rescued Desmond from the well.
Locke to Jack in the ALT: "You don't have a son"...that sent chills.
Kate in that dress lol

...I'm sorry, but when they showed her approaching Jack after the concert had ended and Jack was looking for his "son", and especially when they showed her from the side...hoo, boy. I kept thinking why can't a woman that hot and dressed THAT good ever approach me and say "I've missed you soooo much"? lol
That they actually kept both Richard and Lapidus alive lol.