City of Bones
- Clary and Jace's picnic at the Institute's garden. You can tell that this is definitely the moment where she falls in love with him.
- Clary being accepted into the Institute at the end, particularly the bit where she and Alec make up after spending most of the book being hostile to each other.
City of Ashes
- After acting like a massive jerkass towards Jace throughout the book, Inquisitor Herondale redeems herself in the end when she shields Jace from a demon attack, upon realizing that he is her grandson. She dies knowing that she has at least protected the last of the Herondales.
City of Glass
- Sebastian comforting Clary after her fight with Jace and then taking her for a date the next day. Sure, he turns out to be evil (and Clary's brother to boot), but the gesture still counts and makes you wonder what kind of brother to Clary he would have turned out if he wasn't corrupted by Valentine.
- Alec and Magnus' Big Damn Kiss. Also a moment of awesome, since Alec, who had been agonizing his sexuality his whole life and dreading what others would react if they found out, does it in front of the entire Clave, including his parents.
City of Lost Souls
- Aline revealing that she is dating Helen and that she was encouraged to come out after seeing Alec and Magnus kissing in front of the Clave during the Mortal War.
- Simon coming out as a vampire to Rebecca, who wholeheartedly accepts it and hugs him.
- A villainous example: the revelation that Sebastian wants Clary to rule the world together with him puts his previous Affably Evil actions to her in a different light. Unlike what Clary thought, Sebastian really was kind to her, because, as his sister, he thinks that she is the only one who really understands him, even if he ended up stepping way out of the line.
City of Heavenly Fire
- Clary comforting Emma after her interrogation by the Mortal Sword. As The Dark Artifices shows, this little act is basically what spurs Emma into sobering up and training harder, becoming the best Shadowhunter of her generation.
- Though he can't save him, Jace gives Mark a witchlight before they part ways, to remind him where he came from and his status as a Shadowhunter.
- Sebastian makes amends with Clary and Jocelyn right before he dies.
- Luke and Jocelyn's wedding has a few moments:
- Alec and Magnus reconciling. Although he doesn't want to be immortal, Alec promises to Magnus that he will stay with him as long as he lives.
- Robert coming clean to Alec about his reason for questioning his sexuality and telling him how proud he is of him.
- After his memories are restored, Simon states that though he lived half a year without knowing anything about the Shadow World, he still felt someone was missing from his life. That someone? It's not Clary, Jocelyn, or Luke, all of whom he knew since before he was thrust into the Shadow World. Instead, it's Isabelle.