While Twinsanity is the game that made Cortex into comic relief, what is quite possibly his best moment comes right before the final battle of that game. After being chased and abused by the Evil Twins who used to be his pet parrots, Cortex finally tells them, with no fear in his voice, that playtime is over and to go back into their cage. And it works.
... For a moment, as the cage turned out to be a part of their giant robot. Granted, given the twins themselves were abused pets of Cortex originally, it could be considered equally awesome how quickly they turned the tables when old habits returned.
Madame Amberly says Cortex will always be a little worm to her in the cutscene before the boss battle against her. Said "little worm" defeats the Fat Bastard not long after, getting back at her for all the torment and harassment long ago.
Meta: The fact that, despite it's incompletion, the game's loved and fondly remembered by many fans.
The Final Boss Battle against the Evil Twins as Nina, Cortex and Mecha Bandicoot! Too bad there wasn't any phases with Crash nor Crash & Cortex together... Nevertheless, the battle was awesome.