Jim Cummings' collective performance as Robotnik may serve as one for the entire series. Previously and since, Robotnik/Eggman tends to be portrayed as a buffoon, but Cummings' gravelly, near-orgasmic acting (and, to their credit, most of the writers) made him a real force to be reckoned with.
As well as adding his iconic wacky voice acting into the mix when it was suitable ("SNIV-LEY-EY-EY-EY!!!!").
A meta-example in that the Green Aesop this show gives off is different from others of its kind in that it doesn't beat you over the head with it.
Snively gets a small one in "The Doomsday Project." Robotnik doesn't let him in his emergency escape pod once things take a turn for the worse. That's okay, because Snively prepared ahead of time and had an underground bunker ready for a time like this. Robotnik's escape attempt ultimately failed. Snively's succeeded.
"You don't give me enough credit, Julian."
In Blast to the Past: Part 1, Sonic and Sally travel back in time to thwart Robotnik's revolution against the kingdom of Metropolis and prevent the downfall of Mobius' monarchy. Due to a slight mess up on Sonic's part, they arrive too late to stop the attack and find themselves at Robotnik's mercy when he announces himself to King Maximillion. This scene follows, ending on a cliffhanger...
Robotnik: Your majesty, members of the royal court, heh heh... welcome to Robotropolis, the capital of my kingdom. Ahahahahahaha! Heh heh heh.
Sonic getting the Smart Ball for once in "Sonic And The Secret Scrolls", acting as the more cautious team mate to Sally and the others and eventually saving them once their plane fails. This is also arguably the one moment he gets Sally to admit she was wrong in a situation, and he revels in it gleefully.
In one episode, Robotnik is tricked into falling into a trap by Antoine! That's right, freaking ANTOINE successfully tricked Robotnik into a trap of his own design! Granted, it didn't successfully hold Robotnik for long but the fact that Antoine was able to trap him at all is something of an accomplishment for him.