Helen deciding to leave Joe to pursue a music career in New York. Joe begs her to stay, telling her that he loves her. She quietly declares, "I love you too". . . and leaves. In-universe too, as during the Clip Show where they reflect on their relationship, Joe doesn't want to discuss it and Helen cries so much that they have to stop taping.
The whole hangar scene between Joe and his mother in "Mother Wore Stripes"
Joe: "Yeah, well, sorry does not cut it! Sorry does not give me back my childhood!"
Joe: "I thought that you left because I broke your pitcher....I'd never seen you so mad....when I got home, you were gone."
Joe: "How can you even THINK about marrying Lynch! It's WRONG! Having kids with him, growing old together, that's OUR marriage! Those are OUR kids! That's OUR lifetime! We're supposed to be together. (pauses, then continues quietly) I love you, Helen."
Joe telling off Brian after the latter burns down his house, telling him that he's fed up with his screw-ups and cutting him off.