The guitar duel between Megabyte and Bob in "Talent Night".
Megabyte: I've always wanted to do that.
"Wizards, Warriors, And A Word From Our Sponsor" is Mike The TV's moment in the sun. During a particularly hazardous game, he advertises kitchen products, spews countless corny taglines, and, with a little ingenuity, actually saves Dot, Bob and Enzo from various demons. And even makes a game-winning catch at the end.
Mike:AND THE CROWD GOES WIIIIIIIIIIIIIILD!!!
The Tiff." Bob and Dot have a major spat over Bob's "living on the edge" lifestyle versus Dot's careful schedules. Of course, the two wind up stuck in a game cube together, so after putting aside their differences, they successfully integrate both of their usual approaches to win, with Bob showing shades of The Smart Guy and Dot being a more impulsive Action Girl. It's an awesome sequence for many reasons, primarily in how it shows how much Bob and Dot truly need each other.
Hex: Now I suppose you'll want thanks for all your hard work?
Not only that... She WINS. The Medusa Bug infects the entire system. So Bob gets a moment of his own when he makes the Queen of Chaos realize that she's the queen of a system where nothing will change ever again.
In retrospect, the Crimson Binome. He's one of the few people to have subdued Frisket.
Think about it, not even Megabyte has dared getting too close to Frisket!
The episode that introduced the pirates is full of these. Not only does Captain Capacitor defeat Frisket like it's nothing, Princess Bula defeats Bob in hand to hand combat 'twice', Bob escapes from the pirate's prison and cripples the ship giving Dot the chance to catch up, and at the end once brute force has failed to stop the pirates Dot snatches victory from defeat using her amazing marketing skills and proving her methods to be vastly more profitable than the pirates own. And to make things even more awesome Dot's actions actually are directly responsible for saving all of Mainframe from Megabyte and getting Bob rescued from the Web, due to Captain Capacitor's fondness and respect for her.
Slash gets one in "Gigabyte". The titular virus (a combination of Hexadecimal and his boss Megabyte) drains Hack of energy. This enrages Slash so much that he uppercuts Gigabyte all the way back to Mainframe from the island that Bob was trying to use to get distance between the Principal Office. Despite boxing Bob's plans, this was undeniably awesome. Even more so Slash's justification:
Slash:He hurt my friend.
"Infected": Dot kicking Megabyte's ass with a giant robotic exoskeleton.
AndrAIa having an old west showdown with an infected guardian.
Matrix driving off the web riders by shooting through the a hole in the ship and landing headshots on a few of them.
Bob saving AndrAIa and finally reuniting with Matrix in the web.
Bob merging with Glitch and opening a portal to Mainframe from the Web. As he does so, he restates his format: "to mend and defend."
The opening credits to "Firewall," which is a Shout-Out to the James Bond movie opening titles.
Matrix, back at Mainframe after Game-hopping for all those cycles, fights Megabyte. One of the first things he does is dent Megabyte's chest.
Megabyte goes from looking like he's thinking "I can't believe he fell for that" to "What the hell just happened" and it's wonderfully appropriate.
Honestly, this entire fight scene is awesome from beginning to end, but it's ultimately an Awesome moment for Matrix, who conquers Mainframe's greatest adversary in an even fight - which Bob could never pull off by himself - after ages of just being Dot's bratty kid brother.
In spite of the fact that it ends really badly for Enzo, the various fights between him and the User in "Game Over" are damn awesome. It gets better when later, as Matrix, he eventually gets his revenge on the particular User character that sent him and AndrAIa across the web.
The rematch is especially awesome because of how he wins it. He doesn't shoot him with his gun, doesn't overpower him like he did Megabyte earlier, instead he shows us, and the User, how far he's come since the last time they fought. He dominates the fight, using the skills he's picked up and chaining combos that prove that this time he's the better fighter between the two. And it is immensely satisfying to see.
Little!Enzo's speech to Matrix and AndrAIa in Daemon Rising, after they become infected. Little!Enzo's "What the Hell, Hero?" spiel overpowers Daemon's infection.
Bob calling Turbo out during the My Two Bobs arc after it is revealed that the 'other' Bob was really Megabyte all along.
Bob: "I really don't care what you think about my theories, Turbo. If we had done things your way, Hexadecimal would have been deleted and the entire net would've been destroyed."
After almost two hours of Daemon being a Villain Sue along comes a pissed off Super Hexadecimal who starts smacking her around the city before defeating Daemon's infection of the entire Net and saving EVERYTHING!
Note that not only is she is the first to fight Daemon in a way that actually resembles a fair fight, she doesn't hesitate AT ALL when informed of the Heroic Sacrifice the disinfection of Daemon will require.