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 he is chained to a signpost after he is caught. Homer brings him only a shirt and shoes, and forces him to walk around Springfield this way. After Bart says that this is the worst day of his life, Homer corrects that it is "the worst day of your life so far". 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 again corrects: "best kiss of your life so far."
In the native's medical hut, Homer realizes what his Jerk Ass 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.
Homer giving probably the most poignant line he's spoken in 20 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!
Flanders spending time with Bart after Homer mistreats him.
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.
Homer and Bart reconciling when, after Homer's big apology 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.
Bart: The man knows me.
While everyone waits for the bomb to go off, Comic Book Guy affirms his choices note In defiance of an earlier episode where his outlook was far more pessimistic:
"I've spent my entire life doing nothing but collecting comic books, and now there's only time to say- life well spent!"