Lysander and Tancred rescuing Charlie from the ruin during the ruin game. The storms and spirit ancestors that they summon manage to spook Manfred and Zelda so badly that they are still not themselves for over a week afterwards.
Paton Yewbeam in the first book of the series, when he blows up the lights at the school to force Bloor to hand over Emma's birth certificate, and walks away laughing after he does.
Also when Paton BLOWS UP a sewing machine, kills a 100 year old shape-shifter, and burns down his evil sister's house, all in one shot.
Charlie Bone and the Time Twister Charlie Bone and the Blue Boa
The 'night of wind and spirits' in the third book has quite a few awesome moments:
Olivia confronting Belle/Yolanda in the girls' dormitory, and Emma trying to help her.
When Tancred, Lysander, Billy, Charlie and Gabriel face Yolanda, she tries to hypnotise them and shapeshift at them, but they never freeze (well, except Tancred, who's afraid of spiders). In fact, the most awesome moment has to be Gabriel running at Yolanda after Tancred freezes.
Charlie Bone and the Castle of Mirrors
In the fourth book, the act the good endowed children and Paton pull off to rescue Billy from the Bloors and restore the balance among the endowed children of the Red King.
Charlie Bone and the Hidden King
In the fifth book, ten good children banish Count Harken from the city by walking hand in hand around the tree that is the Red King.
Charlie Bone and the Shadow of Badlock
Emma flying out of school when Tancred is being drowned by Dagbert to get Mr Torsson to rescue him.
Mr Torsson breaking into the school to rescue his son also bears mentioning. He breaks down the main door to the Academy and storms down into the Art basement, creating a mighty big storm and causing chaos in the school. No one can stop him, not even the Bloors. He then confronts the Bloors, with his son in his arms, and yells that they'll pay for what they've done.
Anything involving Lysander and his African ancestors counts as this. Those ancestors are enough to terrify the Bloors and stop them from doing anything.
Due to his powerful hypnotic ability and status Manfred is able to bully just about anyone and get away with it. He's easily able to read Charlie's mind and disconcert him in their first meeting. However just a year later when he tries extracting information again Charlie not only manages to resist him, but steal one of Manfred's memories. Not only that, but later its revealed Charlie's pretty much broken Manfred's hypnotic powers for good.
Amy and Lyell, in the last three books, manage to fool everyone (even the Bloors!) into thinking that they're going on a second honeymoon, so that no one would realise that Lyell is the Red Knight. They go as far as sending fake postcards to Charlie, and planting suggestions in his mind to divert him from discovering the true identity of the Red Knight, in case Charlie is hypnotised by Manfred. None of the other characters have any clue what they are really doing until the final battle is over and the identity of the knight is finally revealed.