Pretty much all of the Professor's scenes but most obviously when he has just returned home with birthday gifts for the newly-created Powerpuff Girls, when he sees them exercise their superpowers for the first time. At first he is struck dumb, but then a loving smile crosses his face. Bubbles receives her beloved Octi as a gift and thanks the Professor, saying "This is the best gift ever, Dad!" The Professor's response? He takes one look at his girls and simply says, "Yes... it is." *sniff*
I will give you extra food of thought: when he's cleaning up the drawings they made, he picks up Bubbles' drawing note which was actually a drawing from a contest held as the movie was being produced . It's basic colorful blobs of crayon of the three girls and their father at the bottom.
Doubles as Fridge Brilliance and foreshadowing but Professor Utonium explains why he created the girls in the first place, "Wow! I can't believe it! I wanted to create some kids I could teach good and bad, right and wrong, and in turn maybe they'd do some good for this terrible town, and now I can! All I got to do is be a good parent!" ...And since the girls eventually end up using their superpowers to fight crime, HE WAS RIGHT!
It's also important to note that this monologue happens before the Professor comes home and sees them using their powers for the first time. Even before he realized that his girls had superpowers, he already believed in all the good that they could do.
After the girls have finally finished their disastrous, city-destroying game of tag and they're still literally bouncing off the walls at home, blissfully unaware of the damage they're done and the trouble that's on the horizon, it's easy to assume that the Professor might snap at them or yell at them to cut it out. Instead, while he's clearly worried and tired, he maintains a stern but gentle tone, playing along with the game of tag for another minute before putting them to bed. It's a very sweet scene, especially when you remember that the Professor's only been a dad for nearly two days. Though, this backfires greatly because he tells them, the town needs to take the time to understand the girls' "specialness"
The girls and the Professor have only been a family for a handful of days by the time the climax of the film gets rolling, which makes it all the more touching to see how much they already care about each other. When the girls first start to hear the people in Townsville in pain from their distant asteroid, they're conflicted on whether they should intervene or not. Eventually, they just try to block it out - until they hear their father in trouble. Then, they react instantly, rushing back to Earth while screaming for him. Even after he doubted whether or not they were truly good, they still do everything they can to save him.
Likewise, the girls react with genuine horror when Mojo threatens to hurt the Professor and don't make any other moves on the villain until their father's safely out of harm's way.
And on the Professor's side, his shout of "GIRLS!" when he realizes they've come back (before Mojo muffles him) is unmistakably happy and relieved. When the girls arrive at Mojo's lair to save him, he also begs them to save themselves, even though he's the only one in the room without powers of some kind and is clearly in the most danger, being used as a Human Shield and all. Even though he doubted the girls and has only had them for less than a week, he's still completely willing to sacrifice his life to keep them out of danger. That moment definitely doubles as heartwarming and a tearjerker.
While it mainly counts as a tearjerker, Blossom tries everything she can to console her sisters when they are lost in the city.
After Mojo has injected himself with additional Chemical X and become a terrifying behemoth, the Professor wants to get out of town with the girls ASAP. However, they refuse and very bravely insist that they have to fix the problem they helped start before flying off to save the day. The Professor watches them go with a proud expression, a tear in his eye. At that moment, it's clear that he's realized that his girls really ARE going to do some good for the town like he wanted in the first place...although not quite in the way he thought.
The Professor and the girls' first "I love you's" as a family.
Professor: I'm so sorry for doubting you! You are good! Good, perfect little girls, and I love you!
Blossom, Bubbles & Buttercup: We love you too!
The ending of the movie. Right before taking the antidote, the citizens form a heart shape around the girls and they are accepted by the townspeople. The narrator also recites his usual saving the day line. It's even heartwarming and nostalgic when you watch it and you're older.
Especially from Ms. Keane, the guys who complained about the car and even Mayor going all fanboy over what they had done. That just shows that they do regret how they treated the girls and want to make it up to them.
How accepting the school children were when the girls were first in class. it just showed how friendly the people of Townsville are despite their not-so-great city at the moment.
Heck, even MitchMitchelson, a boy who abused a hamster in the series, helps them learn how to play tag. Just that alone is heartwarming.
A bit of sisterly love- when the girls are with Mojo at the zoo, a woman drops her baby's rattle. When Bubbles returns it, she snatches it away and mutters about how "all animals should be in cages at the zoo." Blossom and Buttercup both immediately go to Bubbles' aid - Blossom comforts her sister and Buttercup yells after the woman for being such a jerk. Aw!
During the final battle, the Powerpuff Girls rescue a baby from the monkeys. It turns out the baby belonged to the same woman who insulted them, and she finally thanks them properly in the very end.
