When you think about it, the whole basis for the show (for the first three seasons, at least). Michael gives up his chance to get away from his crazy relatives and finally be happy, all because his son was lonely and needed a family.
According to The Other Wiki on Michael's character profile: "Michael's wife Tracey died of ovarian cancer two years prior to the first season. Possibly, as a result of this, he is very close to his son, George Michael..." That alone is beautiful right there.
"Pilot": Michael is upset that George Sr. gave the promotion to Lucille instead of him... until he finds out that it was to keep the rest of the family out of jail, as he was led to believe that it's impossible to arrest a husband and wife for the same crime. It was a hilariously misguided plan based on a faulty premise, but his intentions were noble.
"Key Decisions": Heartbreaking and heartwarming all at once: Michael deciding not to get in the way of Marta and GOB's relationship.
Michael: You gotta put family first. That's the stupid thing I believe.
Michael chastises Lindsay for getting involved with vapid and shallow charity events, especially when she claims to support the wetlands without knowing anything about the cause. In response, she actually visits the wetlands, but then shows up to the bachelorette auction a mess, with no one wanting to bid on her. Michael, realizing that Lindsay finally made an actual effort to be involved with a charity, bids on her so that she won't be humiliated.
George Bluth Sr. occasionally shows that, much as he failed raising his own children, he wants his grandchildren have a better life, as his reaction to GOB sending George Michael to steal documents from a permit office shows.
"My Mother, The Car": The revelation that George Sr. paid off all the other inmates so they wouldn't sexually harass Lindsay when she came to visit him in prison.
"Storming the Castle": The end of the episode is a little bittersweet for Michael, but Lindsay does show him some genuine sympathy, and George Michael cuts him some slack for taking the chair from work. The look on GOB's face when he sees that Marta is the assistant Michael got for the show is also very heartwarming, as is his sheer happiness when he approaches his mother afterward. His happiness then inspires Lucille to accept Buster's relationship with Lucille 2 and have a sincerely friendly interaction with the latter. And, after years of stealing from Michael, GOB finally gives something back.
When Michael catches George Michael in the act of purchasing weed for Buster (who needed it for medical reasons), Buster, not wanting to see his nephew take the rap, steps up, remarking that George Michael was only looking out for him.
The ending. Maeby, after spending the day with Lucille and realising how critical she is of Lindsay, tells Lindsay that she is glad to be her daughter and gives her a piece of jewellery that Lucille always kept from her. Lindsay then hugs Maeby and this shows that difficult relationship aside, Maeby and Lindsay do love each other.
"Public Relations": Michael Bluth gets a publicist to help improve the family's image. He starts dating her but then breaks it off because he is worried about it affecting George Michael. The publicist confronts George Michael and asks him why he is trying to keep his dad from being happy. Michael (without knowing this) takes the publicist out to dinner to try and patch it up where Michael's mother and sister confront her to attack her (she had written an unflattering article about them). Michael tries to stops them, however during the ensuing conversation the publicist mentions what she said to his son.
Michael: You did? You said that to my son...? (steps back) You're on your own. Ladies?
"Beef Consomme": Lindsay helping Tobias get rid of his never-nude affliction, and subsequently proving that regardless of what she says - she does love him, and their marriage wasn't some sort of cosmic accident.
"Staff Infection": When it is revealed that Michael kept many of George Michael's childhood drawings and crafts in a folder in his drawer at work.
Narrator: [George Michael] always knew his father loved him. Now he was holding the proof in his hands.
"Missing Kitty": The fact that Gob is legitimately heartbroken at having to send George Michael away at Michael's insistence, even if he was introducing him to a fairly unsavory life. The narrator states that Gob does sincerely love his nephew.
"Best Man for the Gob": Michael is actually hurt that Gob chooses their father over him to be Gob's best man for his bachelor party, and realizes that Gob is only doing it because he's still desperate for George Sr's approval. After George Sr makes Gob's bachelor party all about pretending to kill a stripper to frame someone else, Michael convinces Gob to stop listening to their father, and Gob tells Michael that he's a good brother and his best man.
"Whistler's Mother": After Michael is freaking out about the botched business deal he made, Lucille, in a rare moment, comforts him:
Lucille: It's going to be alright. Michael: Why are you squeezing me with your body? Lucille: It's a hug, Michael, I'm hugging you. Michael: Yeah, but why? Lucille: Yeah, but I don't get along with my- Sorry. That was a knee-jerk. Lucille: Michael, you made a mistake. You're a human being. But you're so forgiving to everyone else in this family. Try being forgiving to yourself.
The narrator refers to Buster as "someone moderately intelligent", which is about as complimentary as he gets with the Bluths.
The family's reaction to Doctor Fishman revealing that George Sr has died (although he actually escaped out the window).
"Sad Sack": When George, Sr. find out that his wife is in love with Oscar and that Michael can get out of legal trouble if he turns George in. He proceeds to tell Michael to make a deal for himself as he (George) has no more love in his life. The episode ends with George waiting in the attic for the police to show up. Michael comes up and tells him that he did not turn him in, and he is sorry that George feels he has no love in his life.
George: I-I don't feel that way anymore. (hugs Michael) Thanks. It's been a long time since someone stuck up for me (kisses Michael on the forehead).
George Sr: I'm proud of you. Michael: Really? George Sr: Yep. See ya (sprints off).
"Queen For A Day": Michael was frustrated that he specifically ordered his family not to sell their shares as soon as they were unfrozen (even though he hypocritically bought a new car with his share). However, he then discovered that Buster, whose relationship he had ruined so that Buster would be able to clean up the mess the others had created, was the only one who read the note and refrained from spending any of the money because he didn't want to hurt the family. Michael proceeds to tell Buster that he'll sort everything out for him, and that it's okay for Buster to continue pursuing Starla.
Michael: You know, uh, I-I want you to forget about what I said. I was wrong, you two belong together. Iíll take care of Lucille 2 for you.
"Motherboy XXX": When Buster and Michael crash the Motherboy dinner-dance to rescue George Michael from Lucille, knowing how humiliating Motherboy is, Buster also crashes the party because he's angry at Lucille for basically rejecting him because of his hook prosthetic. At the end of all the mayhem they cause, he volunteers himself to dance with Lucille 2 in George Michael's place. He then asks his mother if she'd still dance with him, even with his hook. She puts her scarf around his neck, tells him that he can be Captain Hook and she Peter Pan, and they dance together.
Buster: Yes. I am no different. I am the same old Motherboy, but George Michael still has a chance. Take him.
Subverted by George Sr at the end of the episode. He breaks up GOB and Michael's fight in front of the courthouse (again), and tells them that brothers should stick together no matter what. He then turns himself in so that the family will be free of his crimes, and says that he doesn't want them to visit him in prison this time. And then we see this flashback of George pulling up next to Oscar, who was on his way out of town for good:
GOB and Michael forgiving each other at the end of the episode:
GOB: You know it's true... Everything I do... I do it for you...!
"For British Eyes Only": When Michael tells his father that a mysterious British man has threatened "someone stupid in our family", George immediately says he's going to change his plea to guilty, even though it would mean returning to jail. Michael assumes the threat was meant for Buster, but George suggests Gob could be the target, and actually seems worried - insulting as it it for Gob that his father openly thinks he's stupid, it's just about the only time in the entire series when George shows any sign of caring about his oldest son.
"Prison Break-In": When George Sr. breaks in to prison to stop Lucille from sleeping with Stefan Gentles, and tells her that however lousytheir marriage is he doesn't want it to be thrown away.
George: No one is breaking this family apart, no one.
"Making a Stand": Near the end of the episode, in the Gambit Pileup, when George Sr reveals that GOB told him about his and Michael's plan, Michael attacks GOB, and the two brothers brawl. The fight moves onto the balcony, where Michael is thrown off the side of the balcony, seemingly to his death. The whole thing was set up by Michael and GOB to teach George a lesson, but what's heartwarming is that in that moment, seeing his son thrown over the balcony, George cries out in genuine emotion, "NO!", showing his Hidden Depths.
"Development Arrested": When George Michael finally admits his love for Maeby to his dad, and Michael, instead of being offended and judgmental like George Michael expected him to be, understands his son's feelings and only objects to the relationship because it might screw up their familial bond, which would last longer than any fling would.
"Queen B.": At the end of the episode, when Tobias and Marky realise that Lindsay is on Herbert Love's float running for Congress (essentially a betrayal from Mary's perspective), a float which they believe they have just bombed, their first instinct is to desperately try to warn her, despite her essentially betraying their trust and joining the one person she had promised Marky to help stop.
"A New Attitude": Episode 11 with Gob and Tony Wonder admitting that they have feelings for each other (whether the feelings are of friendship or of love is not 100% clear) and just their whole bonding process, which started more as them trying to avenge each other for whatever reasons but actually grew into something fantastic.