The end of the Dark Star Core/Dark Bowser battle. After Mario and Luigi destroy the Dark Star Core, Bowser finishes off Dark Bowser with five punches, the last one being the sliding punch that you cannot usually use in battle. After Dark Bowser explodes, he does the same victory pose and roar he does whenever he levels up.
It's a tie between the first time in Bowser's Inside Story that The Mario Bros. have to revive Bowser and he turns giant as a result - and then proceeds to beat the stuffing out of his own castle and in the beginning of the game when Peach smacks Bowser halfway across the Mushroom Kingdom, quite literally.
How about when Giant Bowser has to fight Fawfulized Peach Castle, which has a freaking black hole gun that fires at the start of the battle, and again halfway through, and both black holes can suck in either Bowser or Fawful Castle, causing damage. The punch maneuver is your friend in the second half of this battle, as a force field prevents fire damage to Fawful Castle after it takes about 50% damage. Hope you burninated the castle to get Refreshrooms beforehand.
The actual cutscene for this was also pretty awesome. Bowser growing about ten times larger, right outside of Toad Town, with all the Toads running around screaming "It's Bowser!" "Flee!"
As Fawful absorbs the power of the Dark Star, he taunts Bowser about how powerful he is becoming, as he turns to a dark silhouette with red eyes. Then, Bowser steps forward and smashes him in the face, sending him flying.
If you manage to defeat Bowser X, it becomes an awesome moment for you as the Emoglobin host will proclaim "You two, best globins ever!"
It's relatively small, but hearing Bowser say Mario's name. It's not said through a chat bubble or a subtitle, but through his own deep, intimidating voice.