Shrek at the end returning Felicia's ogre doll, and his daughter replying, "Thank you, Daddy!" It is especially moving considering the temper tantrum Shrek WOULD'VE made before he learned his lesson!
Shrek's parting words to Fiona in the altered timeline before fading away.
Shrek (to Fiona): Do you know what the best part about today was, Fiona? I got the chance to fall in love with you, all over again.
Shrek (to Fiona): For so long, I thought I was the one that rescued you, but you're the one that rescued me.
Shrek, even though had been treating Donkey as an annoyance since the first movie, when he sees him again in the alternate universe he desperately tries to get Donkey to remember him. He even sings their song for god's sake!
Near the end of the credits, there is a special message that reads "Heartfelt thanks to the talented artists who worked on Shrek the past decade".
Plus, the credits feature moments from the previous three films.