- Homer has two similar lines in the movie that demonstrate him at his worst and best (respectively). Being the Jerkass that he is after Bart is dared to skateboard through the street naked and is chained to a signpost after he is caught, Homer brings him only a shirt and socks and forces him to walk around Springfield this way. After Bart says that this is the worst day of his life, Homer tells him that it is "the worst day of your life so far", assuring his son that it's not all bad. At the end of the movie, he risks his life and successfully saves Springfield in a flashy display of courage, Marge hops on the bike and they kiss. Marge says it's the best kiss of her life, and Homer playfully tells her: "best kiss of your life so far."
- Before it goes south with the "skateboarding naked" dare, Homer and Bart are actually having a lot of fun together with their dare contest.
- Homer commending Bart for telling Flanders to shut up, after Homer himself did so.
- Flanders offering Bart a spare pair of shorts, after Homer forgets to bring him some after his naked escapades. Later, after seeing Bart staring, upset, at Homer through the window, he tries to cheer him up with a cup of cocoa topped off with whipped cream, shredded chocolate, and a roasted marshmallow.
- Flanders spending quality time with Bart like Homer never did, where they go fishing and then hiking.
- After Bart loses Flanders's fishing pole during their fishing trip, he instinctively recoils expecting the upset Flanders to strangle him like Homer, only for nothing to happen. When Bart questions why Ned didn't try to choke him, Ned tells him the only reason a man should lay a hand on a boy is when they're giving him a pat on the back and gives one to Bart, who, after initially refusing, asks for another one!
- Worth mentioning is the fact that Flanders is such a pacifist that he tries a few times but cannot come up with a reason for choking someone.
- Thanks to Lisa and Colin's efforts, Mayor Quimby fully understands the point about the pollution in Lake Springfield and gets all of the townspeople to clean it up at once. Lenny and Carl managed to plug up the nuclear power plant's waste pipe to prevent further dumping while many other citizens (including Lisa and Colin) are using nets and trash pickers to scoop up the trash from the lake; even Mayor Quimby was able to have concrete barriers installed around the lake along with warning signs to remind everyone else never to dump at the lake again. Unfortunately, this all went down the drain thanks to Homer, who refuses to heed the warnings just to satisfy his selfish needs.
- Marge reassuring Lisa that she can make it through the trauma of having the lake polluted by her father due to his selfishness:Marge: Lisa, come on, we've got bigger problems!
Lisa: But I'm just so...ANGRY!!!
Marge: You're a woman. You can hold onto this forever.
Lisa: *inhales deeply* Okay. - Ned Flanders offering the Simpsons shelter in his home when the mob comes after them, likely risking the mob's wrath for doing so. He does this even after Bart points out Homer would not have done the same for Ned.
- Homer giving probably the most poignant line he's spoken in 18 seasons.Marge: We're homeless! Our friends wanna kill us! Before we can even stay in the same room with you, I need to know what was going through your mind when you didn't listen to me and dumped that silo in the lake!
Homer: *shrugs*
Marge: HOMER!
Homer: (completely sincere) I-I-I don't know what to tell you, Marge! I don't think about things! I respect people who do, but... I just try to make the days not hurt until I get to crawl in next to you again...
Marge: (touched) Awww... (looks at Lisa and Maggie) I mean, Oh. - When the Simpsons make it to Alaska, the border guard gives them $1,000, explaining it's to allow the oil companies to ravage the state's natural beauty. Homer exclaims, "I'm home!" and hugs the guard, who thanks him and lets them through the barrier. Also a Funny Moment.
- In the native's medical hut, Homer realizes what his Jerkass behavior had done: the family is homeless and are federal criminals, Marge and the rest of the family have abandoned him in Alaska, and even if he did enter Springfield, the rest of the town wants him dead. After a Mushroom Samba, Homer comes to the ultimate truth: other people are just as important as him, and without saving the others, he is doomed.
- Upon Marge and the kids being brought back to Springfield by the EPA, they find themselves confronted by Moe in the streets. Despite the fact that Moe was involved with the mob who tried to kill the Simpsons for what Homer did, Moe shows no animosity towards Marge and the kids as he greets them warmly and truthfully explains to them that the townspeople went nuts inside the dome for so many days, and that he has self-declared himself the 'Emperor of Springfield'.
- Bart finding Flanders and his sons in the otherwise abandoned church and asking if he would let him join in with his family before they die. Flanders lets him.
- While everyone waits for the bomb to go off, Comic Book Guy affirms his choices note :"I've spent my entire life doing nothing but collecting comic books, and now there's only time to say- life well spent!"
- Homer and Bart reconciling, first with Homer trying a big and sincere apology and when that fails, he instead offers to let him ride on the back of the motorcycle and carry the bomb to toss it out the top of the dome. It works.Bart: The man knows me.
- It's a minor detail that most people miss, but if you pay attention to Flanders during this, he can be seen smiling. Flanders is truly happy to see them reconcile even after he'd already let Bart join his own family, showing he truly was doing this out of kindness and compassion, and not any ulterior motive, even if he was unintentionally helping drive them apart earlier.
- Martin getting a chance to finally stand up for himself and beat up Jimbo and his gang with a plank of wood, after years of them relentlessly bullying both him and the rest of the children of Springfield was both sweet and awesome.
- After Maggie saves Homer from Cargill by dropping a boulder on his head, Homer exclaims, "Maggie! What a great little accident you turned out to be." Maggie salutes him and leaves. Homer's hardly the best father, but he does try, and so his line can be seen as this in its own way.
- As everyone is cheering after Bart throws the bomb through the hole in the top of the dome, Cletus can be seen hugging Brandine.
- Lisa and Colin reuniting at the end of the film and going out for ice cream actually was kind of sweet, especially thanks to Lisa's excitement.
- Upon Homer and Bart returning following Cargill's defeat, all of the townspeople happily cheered for them for saving the town, having completely forgiven Homer for his actions considering the fact that he took responsibility for them for good. They even cheered when Homer drives away with Marge on the motorcycle, with Lenny giving them a thumbs-up.
- The town bonding together and rebuilding after all they've been through. The crowd scenes of everyone celebrating and working together are a far-cry from the crowd scenes of a crazed angry mob earlier in the film.
- Bart offering Homer a pair of goggles, as a sweet little Call-Back to when he accidentally hit himself in the eyes with the claw of the hammer while working on the roof early in the film.
- Bart's joy at the discovery of, despite all odds and the Hell that the town went through, Santa's Little Helper survived all of the chaos by, in his own barks, "doing things that no dog should do and will haunt him forever", only for Bart to respond with an "I love you" and a hug.
