Pretty much every scene with Superman and Krypto. Highlights include:
Unlike most versions, Krypto was actually in Baby Kal-El's ship when it rocketed off from Krypton. When Jor-El protests, Lara says that their son needs a friend. And soon as the ship entered the orbit, Krypto gave the crying baby a comforting lick.
The entire opening scene of Superman and Krypto's walk, of them flying around and helping people. Really goes to show the bond between them.
Krypto and Ace's talk at the Hall of Justice.
After spending the entire movie being jealous of Lois, Krypto gives her his blessing by helping Superman propose to her.
The entire scene of the other pets bonding with the other members of the Justice League:
Jessica catching Chip from falling.
Merton sharing a slow motion high five with the Flash.
Wonder Woman declaring that PB will make a great warrior and cuddle buddy.
When Aquaman laments that everyone forgets the water guy, Keith proves him wrong and gives him guinea pig kisses which he coos over.
Cyborg giving Mark a fire boost, prompting the latter to cuddle him.
While not a people pet, Ace ultimately decides to give Batman a chance due to the shared troubled backstories and starts licking him, which the latter enjoys. Superman was right. A pet WOULD do good for him.
When Krypto learns Ace lied about the farm for the other pets, he promises to keep it a secret and offers a place at the Kent Farm for everyone once everything is over.
... And then it turns out Krypto doesn't need to keep the promise because all the Super Pets have found their "furever” homes.