Any scene when The Professor fulfills his fatherly role.
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 *
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 CoMA 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.
