The defeat of Ogudomon at the end. The entire battle with him was impressive, but his defeat was worth all the effort.
The impressive collection of digimon who were facing the evil mega was also rather entertaining.
Held prisoner by Goro and with no one having the slightest idea where they were, it was Terriermon who devised the escape strategy for him and Renamon. And it worked perfectly.
In the second story, Secret of the 327th:
The battle with MegaGargomon and Cherubimon against the Zillo Beast.
Aayla fighting against Ventress while the Jedi was wearing a slave outfit (It Makes Sense in Context) and without a lightsaber.
She tops this by later fighting Ventress, Dooku, and Grievous at the same time on her own.
A subtle one: Bly choosing to disobey a direct order, and act like a human instead of droid, so that they would go back to save Aayla.
This foreshadows the moment where Palpatine issues Order 66 and at least some of the clones manage to disobey. True, this is because Bly and the others have just learned some rather important information, specifically that Palpatine is a Sith Lord, but it is still quite an impressive feat for the clones and demonstrates how far they've come.
"I am Aayla Secura. I have survived a brush with the Dark Side and recovered from losing all of my memories. I have leapt out of moving gunships and crossed chasms without bridges. I have escaped from Separatist facilities that were exploding all around me and come out without suffering a scratch. I have flown through space, blasting apart any droid that I find without prejudice. I have battled rancors, survived an assault from a swarm of Gigantoformicums and scared a bunch of pirates away from a farm by making them believe they were being attacked by a ghost. I have ridden Acklay into battle and even gone so far as to befriend them. I have destroyed Geonosian droid factories from within and faced off against zombies and Jedi infected with mind-controlling parasites. I have stood in the face of giant blasts from defoliator cannons and emerged unscathed. I have passed into the Palace of Jabba the Hutt and come out with my sanity intact. I have infiltrated an entire base of Dooku's Dark Acolytes to convert my Master back from the Dark Side and helped him to fight all of them off. I have assisted in diffusing an anti-matter bomb before it could destroy the whole of Naboo. I have fought off powerful ice monsters and run up and down on the back of the Zillo Beast – the most dangerous creature that has ever been born in this universe. I have defeated Asajj Ventress and Count Dooku, and I shall defeat you in just the same way."
Renamon vs. Cad Banes. No weapons, no gadgets, no special abilities or attacks. Just hand to paw combat.
When Aayla is kidnapped by Cad Banes, the clear choices are submit to the torture and share a secret that could alter the entire war if the Separatist find out (and die) or remain silent while suffer intense pain at the hands of the bounty hunter (and die). Instead, she because she has learned to think outside of the box, she decides to pay her captor more than Darth Sideous did and have him both release her, keep the digimon a secret, and start working for the Jedi.
Continuing on the trend of cool moments for Cad Banes, Chapter 151 and 152 has him fighting against Darth Sideous with a combination of gadgets, trickery, and luck. Eventually, Chewbacca had to help him make their escape, but he still held his own against the Sith Lord fairly well until then. Never underestimate the Bounty Hunter.
Chapter 190 of "Secret of the 327th" involves the start of one of the biggest digimon battles yet. This battle includes, but is not limited to, the army Nightmare Soldiers, Belphemon, and GranDracmon against the tamers and their partners, the Digimon Sovereigns, the Deva, and a collection of powerful digimon that were either recruited by the Sovereigns or are friends with the tamers and digimon. Oh, and Behemoth.
Special mention should go to the arrival of Fatemon onto the scene. Both the Biomergence and everything he does from his first appearance to GranDracmon's death.
Jar Jar Binks took out an AT-AT walker by being his own clumsy, accidental self.
Almost any of the fight scenes near the end against the Sith and their allies were amazing, but some of particular interest would be:
Ahsoka against Ventress.
Barris fighting and defeating Aurra Sing on her own.
Durge, who is nearly impossible to kill, fighting against Bane and Sakuyamon until she mode changes and crushes him with a forcefield.
Count Dooku's duel against General Grievous.
Aayla taking on and defeating both Bok and Pong Krell at the same time.
Before that, the Biomergence of Numa and Gabumon to form ZeedGarurumon was particularly awesome. This lesser-known mega digimon appeared on the battlefield and began to completely decimate the enemy, leaving even his allies stunned by his firepower.