Harold: You wouldn't understand! You're not her father!
The potion factory certainly has a couple of moments.
Shrek fooling the receptionist that he, Donkey, and Puss are from the magical workers union.
The trio escaping from the factory with the Happily Ever After potion.
Fairy Godmother's plan to trick Fiona into accepting Prince Charming was very clever, especially for how quickly she came up with it; the moment she saw what potion Shrek had stolen, she saw how she could use its effects to her advantage. She even managed to trick Shrek into giving up and forgetting about Fiona for her own good. If he hadn't coincidentally discovered her meeting with Harold and overheard her plan, the whole ploy would have worked!
The Fairy Godmother orders King Harold (who is already having second thoughts about the villainess's plan) to slip Fiona a love potion so that she'll fall in love with her son, Prince Charming. The King places the potion in Fiona's tea, but finds that he can't go through with it, and gives his daughter a cup of tea that wasn't laced with the love potion instead. His response to the Fairy Godmother's outraged "Harold, you were supposed to give her the potion!" is a smug "Well, I guess I gave her the wrong tea." It's also an awesome moment for the animators, because the scene where he gives her the tea is framed in such a way that it's not obvious which one he gave her at first glance, but one can identify the correct one upon subsequent viewings. Also, a Five-Second Foreshadowing occurs when Charming kisses Fiona, as Harold isn't ashamed or horrified, but watching very closely, because he knows he didn't give it to her.
What's more awesome? Throughout the film, Harold has been abused by the Fairy Godmother and treated like a doormat to her. And in the end, he finally had the courage to stand up to her when defending his daughter.
Shrek's fairytale friends find out by total accident that he's in trouble (from TV footage of him getting arrested), and immediately drop everything to bust him out of jail and help him crash the ball.
Any scene with Shrek riding Donkey as a Stallion.
Donkey jumping over a dozen guards with raised weapons, while carrying Shrek and Puss in Boots.
The Fairytale group really pulled through. It was only by sheer coincidence that they find out that Shrek is in trouble, but as soon as they find out, they busted him, Donkey and Puss out of prison, saving the entire kingdom too.
The entire "Holding Out For a Hero" sequence is one big Moment of Awesome for all the characters involved, as well as often considered the Moment of Awesome for the entire Shrek franchise, if not DreamWorks Animation as a whole.
On the note of said giant gingerbread man when his gumdrop button gets hit by a flaming catapult, he roars like Godzilla and kicks it like a soccer ball to destroy the catapult. Hell, just everything Mongo does in this scene in general! It's also when Mongo stops acting like a goof and starts taking the situation seriously.
Puss in Boots does so many awesome things that it's hard to pick just one. Nonetheless, there's a scene where Puss decides to repay his debt to Shrek by staying behind to stall the enemy guards chasing the heroes and then disarms the guards (figuratively) by making an adorable sad kitten face. Before they can regain their senses, he drops the act, whips out his rapier, and goes ballistic on them.
Puss:(growls)EN GARDE!
The guards defending the castle gate, though unknowingly helping the Big Bad, for successfully holding off what they believe is a legitimate, serious threat to the castle and the people inside.
Guard Captain (With no hesitation): MAN THE CATAPULTS!
Shrek's line when he interrupts Fiona and Charming's kiss:
"STOP! Hey, you! Back away from my wife."
Then there's the implication of the sequence itself. Fairy Godmother has repeatedly told Shrek there is no place for him in her tightly controlled and regulated world of idealized fairy tale endings where everyone is forced to rely on her to meet impossibly high standards of beauty and perfection. Despite this, Shrek continually shows off the qualities of the ideal hero; He fearlessly rides a giant gingerbread man to storm a heavily fortified castle and braves legions of guards sent to stop him from reaching the ball, all in the name of true love. Even as the Fairy Godmother sings about the qualities of her ideal of a fairy tale protagonist, Shrek proves he's "strong, fast, and larger than life."
Fiona's quick thinking after Prince Charming kisses her. To clarify, the only information she has is that the man she's been dancing with isn't Shrek, that Fairy Godmother cried out "She's taken the potion! Kiss her now!", and that once Prince Charming did so, Shrek let out a Big "NO!" and looked defeated. Then Prince Charming suddenly caresses her face as if that were normal. While she does look confused for a few moments, she doesn't blow it by reacting with shock or outrage. And then she not only figures out within seconds what's going on, she takes advantage of it to get the drop on Prince Charming. She then headbutts him and immediately reunites with the man she really loves.
Fiona deserves a lot of credit during this point in the film, because she suspected something was up with Charming claiming to be Shrek from the get-go. She even delayed the kiss as long as possible until she confirmed whether it was really her husband or not. Fiona's not a Neutral Female anymore, she's a clever person who won't take a typical fairy tale trick at face value.
There is also the fight between the Godmother and Shrek's friends; from the Three Little Pigs doing an airborne tackle, the Big Bad Wolf Huffing-and-Puffing her away and Puss and Donkey teaming up to steal the wand. Shows that the Ragtag Bunch of Misfits from the first movie are actually a lot more active this time around.
Fiona correctly calling out both her dad and Shrek for putting themselves ahead of her.
Similarly, Lillian frequently calls out Harold for his atrocious behavior towards Shrek, a son-in-law she barely knows. She even suggests that Shrek and Fiona's subsequent fight is Harold's fault, which is more than Shrek's own wife was willing to admit at that point.
The fact that Shrek does everything in this film to show Fiona how much he loves her. She wants her parents to approve? He'll become human for her if necessary.
In the tie-in game, each level features a Hero Time segment that puts the focus on one playable character at a time. These moments are, without fail, extremely badass for the character in question:
Shrek's Swamp: Needing blackbirds for Lil' Red's blackbird pie, Fiona sings a high note for so long that the birds pop!
Spooky Forest: Donkey rides Dragon to rescue Fiona, who's been trapped in the onion carriage and sent hurtling to her doom. At the very last second, they succeed and safely bring the carriage back down to Earth.
Far Far Away: Shrek thwarts a city-wide riot by himself by throwing all the criminals into a police wagon.
Walking the Path: Puss braves a precarious waterfall path by climbing the nearby tightropes without falling, successfully making a route for Shrek, Donkey, and Gingy.
Jack & Jill's Farm: Gingy endures a dangerous obstacle course filled with flowers and giant tomatoes to get a pail of water.
Fairy Godmother's: Lil' Red faces off against the Fairy Godmother herself to buy Shrek, Donkey, and Puss a few precious minutes to sneak into the potion room.
Prison Break: The Big Bad Wolf climbs the prison tower Shrek, Donkey, and Puss are held in to retrieve their cell key while dodging the bombs coming towards him.
The Mines: Shrek and Donkey successfully rescue Snow White from the Fairy Godmother after chasing her all throughout the mines.
Cookie, Cookie: Mongo successfully opens the drawbridge to the castle while Shrek protects him from water balloons through a nearby turret.
is one big Moment of Awesome for all the characters involved, as well as often considered the Moment of Awesome for the entire Shrek franchise, if not DreamWorks Animation as a whole.