Any Ben/Junior interaction. Especially when he comforts him at a Spoiled Brat's party after she forbids him to see her magic show.
The reason that Junior beats the other little-leaguers up with the bat: they insulted Ben.
Ben is at the end of his rope with Junior and is all set to return him... Until he learns that he's been returned 30 times.
Little Ben Healy: But don't you see? We're doing what everybody else has done to him, I mean it's easy to give up on a child.
Flo Healy: Damn straight it is.
Little Ben Healy: But isn't that what's wrong with the world today? People are just looking for the easy way out, like their problems are gonna go away. Problems just don't go, Flo! You know? So the question here is; what are we going to do with our little problem child? I'll tell you what we are going to do. Something that no parent has ever done for him before. We're gonna love him, Flo. Oh yes, We'll love him when he's bad, we'll love him even more when he gets worse, then one day he's gonna crack and say, "Hey, these people really do love me! They ain't gonna quit on me! I don't have to be bad anymore. What the hey, I can be President of the United States!"
When Beck kidnaps Flo and Junior, Ben is initially ecstatic. He opens a drawer and finds three drawings done by Junior when he enters his room: a three-headed dragon (Big Ben), a hideous creature with a giant mouth (Flo), and the last one a loving, normal human being (Ben). He also finds the dried prune that had belonged to his grandfather and that he had given to Junior as a symbol of the bond between them. Realizing that despite all his bratty behavior, Junior genuinely liked him the entire time, Ben snaps out of his Heroic BSOD and he goes to rescue Junior.
Junior and Trixie making up when they realize Ben and Annie are perfect for each other. Followed by the pair of them making a wish for their parents to get together at the Love Rock, and the ensuing Sleep Cute.