Just after the fight with Plotz and Ralph before the bridge. Everyone is safe and Dr. Scratchansniff gives the others some of the accidentally modified elixir to everybody, and everyone reconciles with each other (no doubt all of them feeling pretty bad for their earlier selfishness). Wakko even helps Plotz by giving the unconscious man some of the now delicious elixir.
To elaborate, Slappy got a new supply of food, and Skippy gets friends his own age.
Mindy finally called her mother "mom", and Buttons got a big plate of steaks as a reward for bringing her home safely.
Rita and Runt FINALLY find a home with Dr. Scratchansniff who also got his elixir right, and Hello Nurse, who becomes a great marketing executive, being respected for her mind instead of just her looks.
The way Acme Falls slowly rebuilt its spirit after just 1 haypenny circulated through town.
Yakko, Wakko and Dot discover their truly royal heritage, and become kings and a queen.
Even Plotz and Ralph, set up as villains early on, but goes through a Heel–Face Turn get their wish, as they start up a hugely successful burger chain, giving them money and power. Well, Plotz did, Ralph already had his wish of being a constable, so he's just given the job of directing traffic.
Their reactions when Salazar orders them to kill The Warners. As much as they were acting like the bastards they were in the beginning, the thought of outright assassinating children absolutely horrified them. The looks on their faces just screamed that they did not want to go that far.
When a guard holds a scared Mindy by her clothes with his weapon, Buttons is shown snarling at the guard doing so.
Yakko's bedtime story to Dot about their parents. Though its syrupy sweetness is Played for Laughs, it's still a charming little moment between a brother and sister.
Wakko's "Wishing Star" song.
The Wheel of Morality actually gives us a heartwarming (nay, a SINCERE!) moral.
Never give up hope.
One quick scene also showed that despite Mindy having been told to give the food for her grandmother, she instead gives it to Buttons, upon noticing that the poor dog has no food in his bowl. Afterwards, he secretly whispers above "thank you" before eating the pie. Say what you will about Mindy, but at least she does care for her dog.
One of the songs, just after the Goodpigeons are ordered to tail Plotz, involves a song about the various characters singing about what their wishes would be, and some are completely altruistic. Dot wishes that she and her brothers were happy, while Wakko wishes Dot would have her operation. Rita wishes a home for herself and Runt, and Runt just wants Rita to be happy. The Goodfeathers wish that all three of them would be respected.
In general, the affection the Warner sibs have towards each other throughout the entire flippin' movie - but especially between Yakko and Dot. Snuggles, tickles, her sleeping in his lap - but the nose nuzzle in her supposed "death" scene is the heart-swelling cherry on top.