Pretty much all of his scenes in The Movie 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 of 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.
Comforting Blossom in "The Mane Event":
Professor: What's the matter, honey? Why are you sitting here alone in the dark?
Professor: It's gonna be okay girls-gah-Bubbles, Blossom, Buttercup! Girls! I-I...I love you.
The Girls: We love you too.
The scene in "Uh Oh Dynamo" where the Professor explains to the girls exactly why he built D.Y.N.A.M.O.:
Professor: Look, girls. Yesterday's horrible, horrible monster fight made me realize something. You girls are everything to me. *Tears form in his eyes* You are my life, and — and I'm responsible for your safety and protection.
Professor: Ah, girls. Yesterday all our troubles seemed so far away. Now it seems they're here to stay. Sitting here eight days a week, everyone seems to think you're lazy. I don't mind, I think they're crazy. But you used to be running everywhere at such a speed. Now you think there's no need.
Buttercup: There isn't!
Bubbles: If we can't stop the Beat-Alls...
Blossom: We're never saving the day again.
Professor: Ohhh, you can't do that! What will Townsville do when they look for the girls with the sun in their eyes and they're gone?
The episode "Powerprof" has one that doubles as a CMoA where, after taking a brutal beating from Mojo, the Professor finds the strength to get up and hand Mojo his ass on a platter after the monkey made the mistake of threatening the girls.
And as he leaves, we find out the whole attack was a plan made up by the girls. That's where we see the true extent of the Professor's love for his children.
The episode "Boogie Frights" has the Professor tell Bubbles that everything is okay after Buttercup scares her sisters. His voice is just so tender and loving...*sniff*
The ending to "Substitute Creature" when after the kids stop the girls from harming Mr.Green, he talks to the girls that judging a person by their looks is wrong. After the girls apologize, Mr. Green hugs them as a token of forgiveness and everyone smiles at the end. Even though the episode counts as Nightmare Fuel, it's really adorable seeing a monster like Mr. Green act so loving to everyone.
A little warped, but after the girls are defeated and seemingly killed by the Rowdyruff Boys the trio then goes over to Mojo's and dump Gatorade over him in celebration like football players would do to their coach and the four of them are all laughing happily with each other. It's strangely touching.
In "Something's a Ms", one moment stands out. The Mayor has just received a ransom message for Ms. Bellum, after to his eyes she had flirted with him... then left and not come back to kiss him it was really Sedusa in disguise. When the girls arrive after being called, he's sitting by a fire, the note in his hands, as he exposits about how the whole reason he's mayor in the first place, and achieved what he has... is because of Ms. Bellum. He confesses to the girls that he has no idea what to do without her, and freely admits later on that he would've paid 50 times the ransom to save her.
"The Best Rainy Day Adventure Ever". The entire episode is pretty heart warming as the girls spend the entire episode 'playing' the Powerpuff Girls. They even sing their own theme song.
In "Octi Evil", after spending the entire episode fighting each other, Blossom and Buttercup decide to make up and work as a team to save Bubbles from HIM, which in turn defeats him.
HIM:WHAT!? Blossom and Buttercup! You're supposed to be fighting EACH OTHER!!!
Blossom: Some things are just more important. Right, Bubbles?
In "Equal Fights", after Ms. Bellum and Ms. Keane make them feel ashamed after telling them that Femme Fatale played them for a bunch of suckers, they tells the girls that while there is injustice in the world, they and the people of Townsville are lucky to have them fight it and encourage them to go out and make things right.
In Dance Pansted the Professor is broken down, humiliated and in tears, their love for each-other is ultimately, what snaps the girls back to the good side and out of Mojo's control.
In the IDW comics, Bubbles and Fuzzy bonding, despite it briefly. Even though said Heel-Face Turn was only due to Him's spell causing his alongside the Gangreen Gang, Princess, and Sedusa's evil to be briefly contained, it seemed like he really started having a friendship with Bubbles.
Afterwards, when the truth comes out, the villains are back to the way they were, and Him's defeated/humiliated once more, Fuzzy, after briefly snapping about some trash on his property, he finds Bubbles' drawn picture of himself and Bubbles which established their friendship and instead of tearing it up. He smiles warmly. D'awwww.