The entire opening battle. Kim kicked butt! Ron even had a hilariously awesome moment. But not just that...following after the opening sequence, with the short revamped-spy movie sounding song-of the original KP theme, complete with awesome color silhouettes of scenes from the episodes of the first few seasons.
Kim: You know what I really hate? Shego: That your date melted? Kim: Nah. You.
Kim then casually kicks Shego off the roof into the side of another building where she gets electrocuted before the whole thing falls on top of her, while Kim stands watching with a Psychotic Smirk, her hair blowing dramatically in the storm.
Actually, the creators stated in an interview that they had to add Shego in the paddywagon last minute because test audiences who saw the first cut didn't see her again and thought she really had been killed, though that was never the intent. A good thing too, the awesome moment would have been killed had Kim suddenly gone through Character Derailment.
Kim:"You're right, Drakken. Boys? Dating? Oh it's hard. But this... is easy!"
We have to give Dr. D his due here. Unlike most of his schemes, he put 100% effort into this: An extremely intricate plot involving a toy sketch by Nakasumi, the brain-tapped plans for Dr. Possible's self-replicating machinery, synthodrone personality upgrades, and an in-depth study of the typical teen girl psyche. Not only did he succeed in distributing and activating his ready-made robot army, as well as completely undermine Kim's self-worth and confidence, but if it hadn't been for Ron complaining about bendy straws and finding out Drakken took over Bueno Nacho, they would've never been the wiser and he would've won.
A equally impressive moment for Drakken is when Shego is trying to decipher his plan but can figure out the connection with all the different plans/studies he's doing. She initially passes it off as being another of his Gambit Roulette stinkers, but Drakken, for the first time, is unfazed by her doubt and even when she lights up angrily when he won't tell her. When he tells her why he won't tell her, Shego's expression tells you the Doc's not playing around this time...
Drakken: Kim Possible is not smarter than you.
Shego: (warily) True...
Drakken: If you can't figure it out, she can't figure it out, and that means...
It's a small thing, but James Possible's complete unflappability when captured by Dr. Drakken in "So The Drama". In their previous encounter, he treated Drakken as a slightly more serious threat, but now he's aware of what a joke he is, and throws Drakken's taunts right back at him.
A bit more subtle: Drakken has captured James to acquire important information from him on cybertronic technology for one of his plans. James has the information saved on his computer, and earlier in the movie after accidentally almost deleting the information, he reassures his wife by saying something along the lines of "No need to worry, I've got it all up here" and motioning to his brain, implying he has everything memorized. Seems like false reassurance, especially considering he was freaking out when he almost deleted the information seconds earlier. But while Drakken interrogates him, he uses voice commands to order the computer to delete the information so Drakken can't get it. Drakken instead uses his brain-tap machine to read James's mind and acquire the information from his memories - and he gets it. James really did have loads of data memorized.
A personal favorite Ron moment for me is a little-noted bit in So the Drama. He's telling Eric about him and Kim just being friends and Eric jokes about Kim being 'a real steamer.' Ron immediately turns on him and says, in a voice dripping with barely-concealed anger, 'Okay, let's not talk about her like that EVER AGAIN!' (and keep in mind Eric is about twice as big as Ron). Doubles as a Crowning Moment of Heartwarming, as it shows at just how much he cares about her.