The entire season is a CMOA since the human protagonists become Digimon instead of having Digimon companions. The humans do more than stand around and cause evolutions; they do the fighting themselves!
Episode 2; Kouji jumping into battle, breaking a nearby pole to create a makeshift quarterstaff, and fighting off a whole bunch of Digimon. And this was before he found the Lobomon Spirit!
Episode 12; Takuya beating Gigasmon using quick-thinking and switching between his spirits.
Episode 14; MetalKabuterimon's debut appearance. Bad luck, Grumblemon.
Episode 20; the battle against Petaldramon when the heroes get their act together.
Episode 22; Kumamon catching Takuya in midair, with one hand. "Sweet grab", indeed.
Duskmon in general is a pretty credible threat, with most of his battles being either a Hopeless Boss Fight or an evenly matched affair. Really, the only reason that he ever loses in the end is that Kouichi's memories of being a human and wanting to meet Kouji are eating away at his ability to fight.
Mercuremon. Between taking out Seraphimon and using Seraphimon's own attack he leaves the other Dark Legendary Warriors still standing at the starting line.
Takuya Defeating Mercurymon in Darkness Before the Dawn; after Fusion Evolving he effortless shrugs off the Strike of the Seven Stars (mercurymon's strongest attack), causing Mercurymon to loose his cool for the first time in the series, before backing the guy up against the coffin he had mockingly made for Takuya and wiping the floor with him.
Episode 33; Loewemon and JaegerLoewemon are able to take down a Cherubimon which the rest of the team had difficulty defeating even when working together. He tackles IceDevimon with the same attack later.
Episode 40; Angemon taking on a herd of angry Centarumon by himself in a good example of the One-Man Army trope.
Episode 47; The final defeat of the Royal Knights, long overdue.
Episode 49; One word Susanoomon! Not only does he show up to kick ass once. He does it AGAIN later!
Episode 50; When things are looking really grim. All the digimon spirits and the celestials show up to give the kids hope and a pep talk.
The crowing moment has to be when the FINAL form of the Big Bad attacks the gang from behind. All of the Legendary Warriors appear and vanquish him for the last time.
Justice Gundam's favourite season, despite all the flak it usually gets, has quite a few CMoA... but the last few episodes were what really got him to favour it. Namely, the heroes defeating the Royal Knights, after having made progress after painful progress in previous fights during the latest 10 or so episodes — they went from not even being able to touch them, to giving them a little pause, to actually harming them, and finally to defeating them both. And then, the final battle against the all-powerful Lucemon himself, with moons getting ripped apart by the villain's unimaginable power; Kouichi's sacrifice, the birth of Susanoomon, and the five kids joining together to destroy Lucemon's Satan Mode, which in this troper's mind erased all the disappointment of Takuya and Kouji hogging the spotlight in the second half. The only other season with an equally epic ending is Digimon Savers!
Nothing could erase Takuya and Koji reducing everyone else to living Transformation Trinkets... but Frontier did have some great moments, like Mercurymon's Xanatos Gambit, Duskmon and Beowulfmon's grand battle, all ten Legendary Warriors coming together to put a beatdown on the Royal Knights, and Gotsumon of all 'mons (for non-fans...Gotsumon is a kid-sized rock Digimon and not anyone's idea of Badass, even though the Frontier version has a few tricks his short-lived Adventure counterpart didn't.) gets to digivolve and get dangerous.
To expand on the above mentioned Final Battle between Susanoomon and Lucemon Shadowlord Mode — it's a BFS-wieldingPhysical God vs Giant Dragon Satan IN SPACE! This sequence alone makes up for every flaw in the rest of the series.
Everything about the Kouji/Kouichi plot, which was foreshadowed as early as in episode two was amazing. The Crowning Moment of Awesome of THIS Crowning Moment of Awesome was when Kouichi sacrificed himself to save the Digital World and almost freaking died in the process. Dark plots and Digimon go hand in hand perfectly.
Some love for the Mercuremon/Sefirotmon mini-arc is in order, particularly Tomoki's fight with Asuramon, and Junpei's... basically it was a fight against himself, and it was badass.
Izumi got hers during the same arc. She eats an apple that makes her relive her issues with making friends after moving back to Japan, while Ranamon gives her a Breaking Speech. Who breaks her out of her spell? Not the HoneyBeemon, not her teammates. Instead, she breaks herself out of the spell by simply vowing that she will make up for her flaws and become kinder and stronger! Now that's a strong will!
A moment for the villains; in the original Japanese, when Mercuremon became Black/Shadow Seraphimon, the music that played when he was beating up Takuya was Requiem. Fans of series get a really threatening villain, and fans of Digimon Adventure can imagine that it is omegamon/omnimon who is doing the beating.
Lucemon's first appearance. He shows up and kills the Royal Knights, who have been beating the crap out of the heroes for the past 10-15 episodes, with ease. Then he No Sells two Mega level attacks and proceeds to smash a moon in half with Takuya and Kouji's heads!!! Keep in mind that the mathematics of the spirits makes it even more major: Each Human/Beast pair of spirits came from a Mega level Ancient Digimon. Logically, that makes their combined strength equal to a Mega (Human=Champion, Beast=Ultimate). Emperorgreymon and Magnagarurumon are each composed of 5 pairs of spirits, making them Mega x5!, So when Lucemon so easily pwned them, he was stronger than that, and he was "just" a Perfect/Ultimate.
They turn it around on him by becoming Susanoomon, who according to the above math, is a Mega x10! That's probably the highest Power Level yet seen in the franchise. How strong is Susanoomon? Some people have mistaken him for an Ultra/Super Ultimate Level digimon but the card game states that he is a super ultimate/mega.
Izumi's is when she got in front of a mirror and modeled/envisioned herself in skimpy bathing suits only two or three episodes before winning an eating contest. Sexy dynamite! Lolicon fanservice implications aside, girls, that is what I call a positive body image!
Agunimon stepping off the dark trailmon after returning from the real world determined to rescue his friends.
Just before that, Flamemon digivolving into Agunimon aboard the Trailmon.
Icedevimon's voice. Frontier may be the closest we will ever get to Christopher Walken voicing an anime character.