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!
Blink and you'll miss it, but when Shrek grabs Donkey and escapes through the window, he takes care to protect Donkey's eyes before the impact. Really, even the fact that Shrek bothers to grab Donkey on the way out at all is pretty heartwarming. Considering that Donkey is not generally considered an asset and Shrek doesn't even try to get any help out of him until he finds Fiona missing from the tower, this decision is more likely based on a) not wanting to leave Donkey in the hands of the abusive witches and b) wanting a familiar face around.
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.
Despite becoming repetitive and tedious, the beginning montage of Shrek and the others' life as a found family is awfully sweet.
Small one, but the alternate world's Puss and Donkey becoming friends so quickly is cute considering the animosity that preceded the real Puss and Donkey's friendship.