Florence's goodbye to everyone in "Flo's Retirement" really stands out.
Dan revealing his true opinion of Harry's style of justice in "The Wheels of Justice: Part II."
Roz, the first to be snarky and the last to ever get sentimental, talking at Dan's funeral with frank honesty about how Dan once risked his life to save her and what a good person he was deep down.
Oddly enough Christine, who was the target of Dan's lecherous advances for years, took his apparent death the hardest of anyone.
This was doubly touching as everyone else who spoke at the service was either unable to think of anything nice to say about Dan or wound up cracking wise about what a pervert he was.
To be fair, knowing Dan that's exactly what he would have wanted anyway.
Eh, sorta. He did rib Harry pretty hard about the ceremony after revealing himself, saying "This wasn't a funeral, Harry. It was a roast." He was smiling when he said it though so odds are he did appreciate the sentiment.
Dan gets a couple of these for the episode "Hurricane pt. 2". First, he comforts a pregnant woman during her delivery. Doubles as a Crowning Moment of Funny when he also gently asks her to take her teeth out of his chest. Then, after things are settling down, and the woman indicates that she wants to name the child after Dan, he tells her the truth about his real name, Rheinhold Fielding Elmore, which he had legally changed when he went to school. It was something he'd never told any of his friends before.
Bull getting drunk and lamenting Selma's death, and his subsequent bittersweet welcoming of Florence.
A later episode shows that Harry was very grieved when Florence eventually died too.
In one Season 8 episode, Dan began having severe insomnia problems as a result of his guilt about sneaking money out of a charitable organization he had been put in charge of managing by Bumbling Sidekick / Eccentric Millionaire Phil The Bum. A hallucinating Dan starts having a Villainous Breakdown in the middle of his speech at a fundraiser, eventually seeing Phil's ghost on the stage. Dan confesses his wrong doing and immediately begs forgiveness. Phil grants it, saying the whole reason he put Dan in charge of the foundation was because he knew how badly Dan needed a chance to improve himself. Dan promises to change and the two hug.
Turns into a Crowning Moment of Funny as we then see the breakdown from everyone else's perspective and see Dan hugging empty air and sobbing piously.
Season 8 ended with Phil the Bum's con-man brother Will swindling the charitable foundation Dan oversaw of over ten million dollars, leaving Dan to take the rap as the authorities were led to believe the two had been working together the whole time. To add insult to injury, he left a note mocking Dan for being a sucker. At the end of the two-part episode which opened Season 9, Will ultimately came back, admitting that Dan's own Heel-Face Turn had inspired his own. He returned all the money with interest, as he'd invested the money wisely over the past few months. Dan was cleared of all charges, dropped all the charges against Will in return and everyone's faith in Dan and human goodness was restored. Rousseau Was Very, Very Right.
Dan actually had several Hidden Heart of Gold moments. In the episode "Married Alive" he courts a homely rich woman and genuinely falls in love with her. When she breaks it off he feigns indifference, but falls apart when everyone but Harry leaves.
In the episode "Paternity" he is confronted by a young boy who claims Dan is his father. When it is determined that he is not his biological father, he befriends the boy anyway and takes him to a baseball game(after of course convincing his coworkers that he is going off on another tawdry escapade).