Quint tearing the glister out of the Gloamglozer in The Immortals. Also, Quint defeating it the first time around while simultaneously having to face his greatest fear.
Twig sky-firing himself and Cowlquape across pretty much the whole of the Edge to reach Sanctaphrax before midnight.
Cloud Wolf going into full stormchasing mode during Stormchaser was hugely awesome. Chris Riddel's illustration, showing him at the helm of the Stormchaser, grinning fiercely despite all the chaotic weather around them, sums it up rather neatly.
Maris arguably has a long-running CMoA when she establishes a home for herself and the children she took under her wing and then turned it into a beacon of hope and safety for the entire Edge.
Twig, with a crew of Banderbears, takes the Skyraider on one last flight, attacking the Tower of Night to rescue Cowlquape. It would be awesome enough just for that, but the Guardians did not think there were any ships like the Skyraider still in existence, and the shear chaos the tower is thrown into makes it even more awesome.
Magda getting herself all the way back to the Free Glades, despite being seriously injured, so she could help Xanth at his Reckoning.
Xanth in Vox, risking his life to save Magda and then refusing to save himself and abandon her when given the chance.
Xanth killing Mother Muleclaw III in Freeglader, turning the tide of the Battle of the Luftwood Mount single-handedly thanks to the shrykes' turning on each other without her leadership.
Hekkle the shryke-mate in The Last of the Sky Pirates has several awesome moments. He is a capable Guile Hero, leading Rook and the others disguised as sooth-sisters through the shrykes' city. Then he stands up to a logworm in the Deepwoods to buy them time to escape, and escapes it himself off-page. Considering that male shrykes were previously depicted as weak and subservient, Hekkle is quite the badass.
Maugin, all things considered, is easily one of the most Badass characters of the entire series. The first example, an in-universe story in the Twig trilogy, refers to her lowering herself over the side of an out of control ship, in a storm, to knock chunks out of the rock keeping it afloat, thus saving everyone aboard.
In Clash of the Sky Galleons, she comes up with an even more extreme solution to a similar situation; covering her suit with tar and striking sparks to set herself on fire and then riding out the storm clinging to the side of the rock, providing the heat to stop it going out of control. Even with her heatproof suit she was burned extremely badly, but once again saved the entire ship.
Her own origin story did it again; upon realizing that Ramrock, the previous stone pilot, was dead, and Wind Jackal needed more lift from the rock, she took up his hood and gloves, and then, going entirely off what she'd seen Ramrock doing, cooled the rock so suddenly that the Gailrider sliced right through the opposing league ship as it rose. And that from a girl who had never even seen a flight rock before that day.