"The Girls of Route Canal", in which Duckman tells his sons the story of how he met Beatrice.
Near the end of "Cellar Beware", Duckman throws himself on top of a bomb — and even though it didn't end up exploding, Duckman "sacrificing" himself willingly to protect his family tugs at the heartstrings a little.
The end of "Sperms of Endearment", when Duckman and Bernice walk together in the park and engage in a venom-free exchange of their usual insults.
After being driven to the brink by his various future-selves in "The Once and Future Duck", Duckman finds himself face-to-face with a past version of himself — from the day of his wedding. When Past!Duckman asks if he and Beatrice will grow old together, Present!Duckman tells him the truth: "You're gonna love her until the day you die."
Past!Duckman: ůmaybe I don't need to know any more than that.
"Ajax and Ajaxer" ends with a dedication to the late Dana Hill.
After Duckman reveals why he was such a jerkass to King Chicken as a child, they bond in King Chicken's rec-room/Duckman-murder-shrine. After so many implied years at each other's throats, for the truth to finally come out and for them to be able to be in a room at the same time, even if it involved copious amounts of alcohol and King Chicken having an affair with Bernice, was a nice development.
Too bad it didn't stick by the end of the episode, though...
The ending of the very first episode qualifies as one.