How about the ending when Gosalyn learns Darkwing survived the massive explosion and has even taken up a civilian identity so he can adopt her?
Meaning that she and Launchpad are his "really really close friends"! Remember from earlier?
Gosalyn: You mean you don't take off your mask for anyone?
Darkwing: That's right, not no one, not never.
Gosalyn: What about a really, really, really close friend?
In Darkly Dawns the duck part 2, Darkwing is locked in prison and laments how he screwed up and has no one to ask for help when Launchpad breaks in. And before he was coming to bail DW out of Jail even though Darkwing was so mean to him earlier. What seals it is how surprised, yet happy DW was to see him. Later, he’s so happy when DW finally accepts him as a sidekick.
In "Life, the Negaverse and Everything", after talking to the Friendly Four, Darkwing still has every intention of going back to his own universe without trying to help them, until he sees Nega-Gosalyn again.
Darkwing: In the Negaverse, there's never been a Darkwing Duck to guard the city *gulp* or a Drake Mallard to be a father. For you, Gosalyn, I'll stay.
At the end of the same episode, Darkwing feels bad about leaving Nega-Gosalyn behind, but she assures him that she'll be fine and that she has four other Darkwings (referring to the Friendly Four dressed as Darkwing).
Also in "Quiverwing Quack," where Darkwing forbids Gosalyn from assuming her new superheroine identity because he's afraid for her safety:
Gosalyn: You never treated me like a hero! You just treat me like your baby girl!
Darkwing: (softly) Because you are.
Hell, pretty much any interaction between DW and Gosalyn that isn't intended to be comedic. They may be after each other like cats and dogs half the time, but this troper is hard pressed to think of an animated work that captures the love between a father and his little girl like this series could.
Gosalyn giving all of her Christmas presents to the Muddlefoots after they're stolen by Bushroot.
Darkwing: Poor little guy [Honker].
Gosalyn: He is not! I mean... you can't be poor... if you have friends.
"The Haunting of Mr. Banana Brain", Paddywhack decides he take Gosalyn as his protege prankster and tries to suck her into his jack in the box. In moment that has no comedy to it, unlike the rest of the episode, Darkwing jumps to catch keep from getting pulled in and tries to secure himself with his grappling hook, and when Launchpad says he can't hold both them, Darkwing ties down Gosalyn and lets himself get pulled him without a second thought.
In the new comic series, Darkwing, having been out of work for a year, is now in a St. Canard where no one remembers him. When he finally puts the suit back on to investigate Quackwerks' security robots, he is caught, mistaken for a singer, and sent to perform at a retirement party. When he finishes, the retiree tells him that he is suspicious of the robots and someone should investigate, leading to this exchange:
Darkwing: But no one knows the security codes to get i—
Thwackstien: 2447-6-3253. My memory's better than most, son, and I know a hero when I see one.
Darkwing trying to break the brainwashing on the catatonic Morgana in issue 5 of the comic. He succeeds, taking the entire issue to do so, also revealing that without Darkwing, Drake is a duck without a driving purpose. In the end, just about to give up, he tearfully says to her that if he never quit, she would never have suffered. The tear breaks her out of it.
From the end of the "Crisis On Infinite Darkwings" arc: as the hundreds of assembled Darkwings attempt to battle Paddywhack, they're not doing much damage. Then Gosalyn shows up, and as every single Darkwing catches sight of her, this produces a massive flood of love and positive emotion, that Morgana is able to channel to defeat and imprison Paddywhack effortlessly.
In ‘Can't Bayou Love’ DW doesn’t even hesitate to go and save Launchpad when he discovers his friend has been kidnapped.
In ‘Waywater Ducks,’ DW was honestly concerned about Launchpad when he, LP, was being approached by a sand storm. At the end of said episode, Launchpad is about to explain that Darkwing is the real hero, but he interrupts and instead says that he is the luckiest sidekick in the world. He then admits that being a sidekick is harder than it looks. (He slips back into the status quo, but it was still sweet.)
In U.F.Foe, when Launchpad is "captured" by the aliens DW runs after them ordering the aliens to release his sidekick. Later, when Gosalyn and Drake have seemingly forgotten about Launchpad due to the Aliens erasing their memories, Drake remembers Launchpad when he finds Launchpad’s Teddy bear, which in itself is adorable.
Little Launchpad earns an "aww!" by himself, but seeing him play with little Tia is just so cute!
There's an episode where someone tries to frame Herb Muddlefoot for a series of crimes. When SHUSH tell Darkwing to investigate, DW refuses, stating that Herb would never do such a thing. It's heartwarming to see that even though DW finds him annoying, he never once doubts Herb's innocence.
"I have a better memory than most people think... and I know a hero when I see one."
"You were always my Superhero."
"Rest your head, little girl blue, come paint your dreams on your pillow. I'll be near to chase away fear, so sleep now and dream till tomorrow." (All of Darkwing and Gosalyn getting to know each other in the first story, really, but it's hard to call that a moment.)
There are a few good moments in Life, the Negaverse and Everything. When Darkwing realizes that the Good Gosalyn's guardian is Negaduck, he decides to stay in the awful reality for her sake. And then at the end of the episode, after defeating Negaduck with the help of the Friendly Four (dressed in Darkwing Gear) and is about to head home, he asks if Gosalyn will be alright. Her response? "I have four Darkwings to take care of me now!" All while the good incarnations of his worst enemies merrily wave goodbye. Aaaaw.