Vince finally getting Stuart to dance with him on the podium.
Stuart and Vince's relationship in general. Yes, it's messed up, with Vince being so madly in love with Stuart that he is incapable of telling him "no", and Stuart taking advantage of Vince's good nature at every opportunity to dodge responsibility. Stuart also tends to be dreadful at displaying affection in a healthy way (despite not admitting to wanting a relationship with Vince, he is incredibly jealous when Vince actually gets a steady boyfriend... but instead of being honest about it, he merely gets into an increasingly petty grudge-match with said boyfriend). However, on the rare occasions when they both manage to deal with their issues long enough to tell each other how they feel, the results are incredibly heartwarming.
Also heartwarming in an odd way is their almost-sex scene in the second season. The series takes place in a world of constant, emotionless one-night-stands from which partners tend to emerge not knowing each others' names, let alone having any sort of relationship. Stuart and Vince make a studied effort to resolve their Unresolved Sexual Tension... which leads to a scene featuring them slowly removing their clothes without breaking eye contact, and eventually simply sharing the bed without having sex, in stark contrast to the graphic, impersonal sex scenes in the rest of the series.
Stuart proving how well he knows Vince by listing in order all of the actors who have played the Doctor (as of 1999).
The conversation between Stuart and Hazel in which Hazel finally confronts Stuart on the sixteen-year-old question of why he has never resolved his Unresolved Sexual Tension with Vince, and he finally admits what we all knew... that his feelings for Vince are far too romantic and tender to want to relegate him to the same level as all of Stuart's emotionless one-night-stands. Also, the rather sweet, awkward kiss(es) between Stuart and Hazel, which he uses to illustrate the point that true, deep love for someone doesn't always lead to sexual desire for that person.
And then Stuart's decision to "see" whether he could find it in him to have sex with Vince, which leads to them slow-dancing and eventually checking out a room together, which leads to the above-mentioned averted sex scene.
When Brian finally tells Justin "I love you" after Babylon is blown up.
The rooftop scene from the pilot. Brian's freaking out over the birth of his son, and Michael's there to tell him he'll be fine.
Brian: Let's fly, like in all those comic books. I'm Superman! I'll show you the world!
Michael: Why do I always have to be Lois Lane? (turns around and hugs him) Congratulations, Dad.
Episode 19 of season 1. Though the first part of the episode is heartbreaking, Michael turning Brian's offer of sex down and supporting him through the death of his father is lovely. And the scene in the bowling alley where Brian (and his father's bowling ball) beat the team of homophobes is perfect.
Bowler: Fucking fairies.
Brian: Yes, the fucking fairies have scored. The fucking fairies are jumping up and down. The fucking fairies - are gonna celebrate. (dips and kisses Michael)
As is the end if the episode where Brian throws his father's ball away (symbolically letting go of all his anger and resentment over the abuse) and Michael hugs him while Badly Drawn Boy's "The Shining" plays.
While the callback to Justin's bashing in season two is heartbreaking, Michael and Brian's friendship turns it to something heartwarming. Michael's boyfriend Ben is in the hospital, and Michael doesn't think he'll be able to hold it together. Brian reminds him that when it was Justin lying there, Michael was strong for him and he can be strong for Ben.
When Ted takes Blake under his wings in the first season, and when Blake does the same for Ted in the fourth.
Tracy standing up to Michael when the coworkers make fun of homosexuals, despite Michael having lead her on. A hell of a friend.
A quarreling between Ted and Emmett for Emmett cheating turns into Ted assuring Emmett he is still there as a best friend, too, and his flaws are also a part of the personality Ted loves, as his friend and as his boyfriend.