Crunch finally getting to show his stuff in the ending to Tag Team Racing, by ripping off a large sheet of hard steel from the ground to shield the bandicoots and Pasadena from Cortex's laser attack. This culminates with Crash blocking his machine's engine with a well-thrown hen.
In the end cutscene, they mug Emperor Velo for his sceptre. Yeah, it ended up going wrong thanks to Tiny, but they still overthrew the dreaded ruler of a freakin' galaxy. Revenge at its sweetest.
A minor one, but check out the opening intro, when Velo is establishing the two sides are hostage in his arena, most of the comrades on either look bewildered or shocked. Crash however is standing in front of Coco while shooting Velo a Death Glare, and Cortex just looks bored off his ass from dealing with another Big Bad Wannabe trying to take his position.
This is repeated after Krunk's elimination. Most of the teams, even the villains, look unnerved by Velo's power over his competitors. Crash meanwhile just looks calmly sorry for Krunk, while Cortex just gives an unimpressed look.
Cortex: I, Neo Cortex, am your ruler. You will look up to me! Hahaha!
An understated one, but Aku Aku saving Crash from being sucked into N. Tropy's vortex in N-Tranced. This (and Fake Crash) were a vital Spanner in the Works for the villains' plan, so Crash could rescue the others.
Also a bad guy moment in turn, within seconds, N. Tropy caught and neutralised two out of the three bandicoots, and just barely failed to capture Crash. A Near-Villain Victory within the opening moments of the game.
Coco, despite often relegated to an NPC, has some understated Awesome Moments.
In response to Cortex's above moment of triumph minimising the Earth in 'The Huge Adventure Coco, in what appears to be a short span of hours or even minutes, creates an invention to counter it and grow the whole planet back to normal.
In The Wrath of Cortex she outruns a tsunami. On a scooter.
In Titans she also stops Cortex's Doominator with a single twist of her Transperlooper ("the purple thingy"), which Crash conveniently had in his pants the whole time.
The latter case also came after Crash spending the entire game in Big Brother Instinct mode and barging through all of Uka Uka and Nina's forces to rescue Coco. He's vacuous and immature, but you do not mess with Crash's little sister.