In the opening to "Robotnikland," Robotnik beans Sonic with a monkey wrench mid-Spin Attack.
Sonic and Tails defeating Supreme High Robotnik (who has all four Chaos Emeralds) with four versions of themselves from the previous episodes in the story arc.
Robotnik actually getting that far is something of an accomplishment for him, especially in the manner he outsmarts Sonic four consecutive times over to steal them, and then handily defeats Sonic and Tails in their first bout. Not-So-Harmless Villain indeed.
Tails gets an epic but tiny one in "Hedgehog of the Round Table", where he manages to catch the Chaos Emerald of Invincibility, and promptly uses it to turn himself into a giant muscle-bound fox. He then utterly trashes Scratch and Grounder.
Sonic's escape from Robotnik's prison in "Sonic Breakout".
Mass Transit Trouble is a pretty epic episode...
Despite being the most comedic depiction of the character, Robotnik's plan proves he'a Not-So-Harmless Villain. By having his minions attack three different locations far away from each other as a cover for planting bombs at said locations set to go off at the same time.
Sonic truly earns his title of "Fastest Thing Alive" by managing to go each location twice despite the strain it puts on him.