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.
How excited Donkey became when Shrek told him he was married and had kids. It's just so sweet. He wasn't even weirded out by the idea of marrying a dragon and having mutant babies.
Seeing the triplets and the Dronkyes' playdates is very adorable. True it gets on Shrek's nerves but it's so sweet seeing them playing together and having fun day after day. It's more than likely that they end up becoming really good friends like their parents.
It's actually quite sweet that what sets Shrek off is when Rumple taunts him about the fact that Shrek's children do not exist.
Rumpelstiltskin truly loves his goose Fifi, since he doesn't abuse her like he does the witches, and he reacts with horror when Fifi disappears in the alternate timeline, and again when Fiona blows her up in the present timeline.