In a call back to a Sonic SatAM plot, one episode has Robotnik challenge Sonic to a race. Sonia and Manic, figuring Sonic couldn't resist, show up to try and rescue him... except he knew it was a trap and didn't show, and they have to be rescued.
Bartleby Mink setting aside his aristocratic lifestyle to defy Robotnik near the end of the series.
Robotnik has an awesomely evil line in "Tangled Webs":
Dr. Robotnik: When we find it, "Sanctuary" will become... "Cemetery!"
Dingo nearly destroys Mobius when powered by a Chaos Emerald. This, might I add, was about ten years before Sonic Adventure.
The hedgehogs redeeming their evil counterparts in the mirror universe episode.