When Marjane visits her uncle in prison. Especially when he gives her the swan he made out of bread. Later, he makes a second, smaller one - the first one's niece.
Marjane then telling God to Get Out! of her dreams, showing that she has lost her faith and given up her dreams of being a prophet.
The Communist girl Niloufar's death. She was hiding in the passport maker's apartment due to her beliefs, living in his basement. Due to bad luck, and prying guards, however, she gets caught and executed, with her host's apartment ransacked. In the book this is actually shown; in the movie Nothing Is Scarier as the passport-maker calls Marjane's father.
The scene where the Baba-Lévis are revealed to have been killed. Especially Marji's reaction to the daughter's death.
Marjane's great-uncle dying because he didn't receive his passport in time to fly to Germany and get an operation there.
Marjane's mother in Mama Bear mode when they learn about the virgin girl Niloufar who was forcibly married and raped so she could be executed. She tells Marjane while shaking her that such a fate could happen to Marjane if she keeps speaking out.
Her parents make the decision to send Marjane to Austria, for her safety but it's not easy for any of the parties: Marjane turns around to wave goodbye one last time and sees her mother has fainted.
In Vienna, Marjane decides to not do drugs because she doesn't want to be a vegetable. After her boyfriend Enrique reveals he's gay and breaks up with her, however, she starts trying hash and marijuana at an anarchist comunne. She even starts dealing drugs to friends as a favor. This leads to her school dean reprimanding her, and her mind going up into smoke. She mentions that it's only thanks to her mothers prayers to God that she passed her exams and graduated.
Marjane's heartbreak after catching her boyfriend Markus in bed with another woman on her birthday, followed by her Heroic BSoD and catching near-fatal bronchitis while homeless on the streets. As she sums it up, she had survived a war that had torn her country apart, but a "banal love affair" nearly killed her.
After all that heartbreak, a doctor tells Marjane that she can't smoke cigarettes, since the risk from her bronchitis would kill her. After booking a flight home with her parents' help, Marjane buys a pack of cigarettes and says the risk of killing her was better than confronting her shame. She had made nothing of her life abroad.
Marjane's internal round of Misery Poker after she returns to Iran. She refuses to tell her parents why she vanished for several months, since they barely survived a war, with tens of thousands dead, and an entire country to rebuild. Even though Marjane's pain is present, she believes it pales in comparison to the horrors of war.
Likewise, Marjane's failure to climb out of her continuing depression, even when consulting several therapists. It takes a Happily Failed Suicide to get her on the right track again.
The entire Iran-Iraq war as a whole and it's combatants, both in book and real life.
When Marjane lies so that another man gets in trouble, to hide that she was wearing makeup in public, she laughs about it to her grandmother. Grandmother gets angry, and gives her a What the Hell, Hero? speech about endangering another person recklessly, and that her uncle didn't die so that she'd have a choice to be spoiled and inconsiderate. Grandmother only forgives Marjane when the latter speaks up at a university forum about the double standards of the dress code.
The fact that her marriage with Reza failed. In the movie it's glossed over, but in the graphic novel Marjane mentions that she needed to believe in love after the disaster with Markus. She and Reza were polar opposites, which was what they liked about each other.
The final panel of the series, where it's revealed that Marjane's grandmother passed away two years after Marjane left for France. "Freedom always has a price..."
Something from the comic that was Adapted Out from the movie involved the Satrapis' housekeeper, Mehri. Mehri was brought to Tehran from a village in rural Iran to work for the Satrapi family. One day, a neighbor confronts Marjane's father that his son is courting the Mehri, and demands that Marjan's father so something about it. Marjane's father than has a heart to heart with the boy, and tells him to forget Mehri, since he's a middle class young man who has a bright future ahead of him, while Mehri is an illiterate peasant, who will likely spend the rest of her life as an illiterate maid. One panel later, shows Marjane trying to console the heartbroken Mehri.
Marjane meeting God and Karl Marx after her suicide attempt. God tell her that she has a lot in her life to live for, and sends her back.
Jasmine petals fall throughout the entire end credits.
Young Marjane: Grandma, you always smell so nice. How do you do it? Grandmother: Well, I'll tell you. Every morning, I pick fresh jasmine flowers, and when I get dressed I put them into my brassiere. That way, I smell nice all day.
Because of telling her stories, Marjane can never go back to Iran.
A behind-the-scenes film shows the real Marjane Satrapi, author of the book and co-director of the film, directing the recording session for the final scene. As evidenced by the numerous packets of used tissues around her, this was clearly not easy for her.
In real life, the war was pretty much a complete loss for families and their young sons as many enlisted to fight hopelessly in what was a pointless war. Throughout the book, the reader is given a glimpse at streets named after dead combatants and post-victim suffering, and this is indeed  as many neighborhoods still have pictures of young men who went out to the front and never came back.