These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Accidental Innuendo: The Absent-Minded Professor Von Schlemmer had a moment of the sort. Robotnik has him tied up, and he asks him what he can do to get Von Schlemmer's invention to work. He replies "I'll never tell you...unless, of course, you fiendishly torture me." Er...
The bounty hunters from "Sonic Search and Smash Squad", largely due to their reappearance in Dr Robotnik's Mean Bean Machine, a rather extreme example of the trope since outside the game, most of the characters only appear for all of a couple of seconds in the show itself.
And, of course, the gooddoctor himself, Robotnik, who´s far more popular than the show itself.
Evil Is Sexy: Catella, the co-antagonist of the episode "Zoobotnik."
Family-Unfriendly Aesop: The show has a couple of real winners when it comes to its attempt at giving kids helpful advice. One segment advises kids against running away from home by having Coconuts try it, and Sonic remind him of all the good things Robotnik does to take care of him, and how no one will be there to do those things if he runs away, to convince him to go back home. The thing is, Coconuts is The Unfavourite among Robotnik's creations, and spends most of his time taking abuse and doing chores to clean up after the rest of the "family", so basically the message comes down to "Even if your family is abusive, it's better than risking it going alone".
Harsher in Hindsight: "Mass Transit Trouble", an episode about Robotnik attempting to bomb three separate transit stations, feels darker than the other episodes because of this trope. It doesn't help that Robotnik and his henchmen are far more competent than usual.
"Zoobotnik" when taking into consideration the "Sonic Sez" segment about sexual harassment. Catella the intergalactic huntress falls madly in love with Robotnik because of how evil he is. Robotnik doesn't feel the same way, but he's too scared to say anything because Catella won't keep her hands off him and is repeatedly manhandling him. In fact, her treatment of him could be considered, barely mind you, g-rated dry humping.
Robotnik remarks in "Full Tilt Tails", "No wonder people say I look just like Santa Claus." In "Sonic Christmas Blast" three years later (with Long John Baldry reprising the role, no less), he becomes Santa Claus.
In "Lovesick Sonic", when Tails is thrown underwater, a fish asks if Tails can swim. He tries using his dog paddle and says, "Not very well," before flying out of the waterfall. Then came Sonic 3 where Tails can actually use the dog paddle to swim, but only for a short time, as he will tire himself out if he swims too hard.
Narm Charm: There's so much in this show it's not even funny. It's hilarious.
The Scrappy: Sonic could be seen as this as he sadistically tortures Robotnik, Scratch, Grounder, and Coconuts. Even when Coconuts decides to run away and possibly be good, Sonic tells him to stay with Robotnik. Not to mention he slams on bar tables, insults the bartenders, and whines while he waits. What a jackass!