City of Bones:

Simon undoubtedly got one when he pretty much silences the Shadowhunters' dismissal of his "mundane" status by destroying a Greater Demon. By firing a standard bow-and-arrow, smashing out a skylight, and killing the thing none of the other three trained Shadowhunters could kill...with direct sunlight. It was so...frickin'...badass.
- You really have to give it up to Clary's mom for the brilliant choice of hiding place for the Mortal Cup: Inside the Ace of Cups in the deck of Tarot Cards that she gave to Dorothea.

City of Ashes:

Jace tops all his impressive physical and battle feats with an emotional Moment of Awesome when he saves Simon's life by slitting his wrist and letting Simon drink his blood until he was recovered, even though he knew Simon could easily kill him this way.
Clary gets her own when she taps into the true potential of her rune power by drawing a rune that completely destroys Valentine's ship. She reduces it to scrap metal.

Alec gets his Moment of Awesome when, after hiding it for almost three books, he finally outs himself by kissing Magnus. In front of a huge crowd of Downworlders and Shadowhunters, including his parents. Doubles as a Heartwarming Moment.
Clary's defeat of Valentine.

Simon's sister Rebecca accepting Simon's vampirism and assuring him she loves him no matter what is massively understated and normal compared to all the overblown battles raging around the rest of the series, but it's all the more amazing because of it. There's no hysteria, no accusations of being a monster, there isn't even a noticeable hesitation once she gets over her justified initial shock that vampires exist. If he's still her brother, then she still loves him.
- And right before that, she's enraged at the thought that their mother may have brainwashed or harmed him in some way. Her tone makes it clear that if this had been the case, it wouldn't have gone well for their mom.