Clippy, of all people, holding his own against the Chosen One, with only the Animator backing him up (and only during part of the fight at that), probably putting up a better fight than all the desktop icons combined. He even survives a direct blast from the Chosen One's fire breath.
The fight between the Dark Lord and the Chosen One.
The massive computer-breaking destruction wrought after the Chosen One and the Dark Lord team up.
The Animator forming bullets out of nothing but text.
Animator Vs. Animation 4
The stick figure resisting having it's task ended..
The stick figure successfully "killing" the Animator (destroying the cursor), something none of its predecessors managed without destroying the computer wholesale.
The Animator's mad keyboard skills when he opens Control Panel and changes his cursor theme.
At last, the Animator makes peace with one of his creations.
Animation Vs. Minecraft
The final battle, full stop. Possessed!Red is approaching the main desktop in his obsidian mecha, and his friends have lost all their armor, all their weapons, and are down to half a heart of health each with no way to restore it. Downer Ending? Nope, they improvise with what equipment and materials they still had and what they learned via experimenting earlier, and win!
Special mention goes to Orange taking down the mecha by building and laying a mine track and minecart right under its foot in the span of a few seconds. And then Blue destroying the mecha by dropping two lumps of dirt, planting two trees in said dirt, and using bonemeal on the trees with the result that they instagrow through the mecha and blast it to bits. Again in the span of a few seconds. While said mecha is falling straight towards him. Quiksilver would be proud.