Adaptation Displacement: While the show hasn't eclipsed the Sonic games themselves, people are much more familiar with Scratch, Grounder, and Coconuts here to the point that some think they were created exclusively for the show, even though they're actually all based off enemies from Sonic the Hedgehog 2.
Cult Classic: The show has a sizable fanbase. Most of its fans grew up with it.
Designated Hero: Sonic's attitude and mischievousness is amped a fair degree in this series, sometimes making his role as a hero pretty questionable. Though this is balanced out by his selflessness and Big Brother Instinct towards Tails.
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".
In another, Sonic and Tails are surrounded by enemies, so Tails suggests calling 911. Sonic shoots down this idea, saying that 911 is for real emergencies. In other words, being attacked by people who wish to kill or seriously harm you is not an emergency.
"Mass Transit Trouble", an episode about Robotnik attempting to bomb three separate transit stations, feels darker than the other episodes because of similar bombings in real life. It doesn't help that Robotnik and his henchmen are far more competent than usual.
In "Sonic Breakout", Robotnik imprisons Sketch Lampoon for making fun of him in a satire based on Humpty Dumpty. This is less funny to watch after the Charlie Hebdo attack in 2015.
"Zoobotnik" when taking into consideration the "Sonic Says" 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", 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.
The way the sloths talk in "Slowwww Going". Fast forward to March 2016 with the Disney's Zootopia featuring sloths talking in a similar manner.
At one point, Robotnik kidnaps Sketch Lampoon, a comic artist, to make him create stories where he's the hero, and advises Sketch to make him look like a more muscular Top-Heavy Guy. Sonic Boom's incarnation of Eggman is a Top-Heavy Guy that looks less fat than any previous incarnations.
Coconuts, so very much. Especially in the Sonic Says segment of "Tails' New Home".
Scratch and Grounder are only marginally less pitiful than Coconuts, if anything their higher position leads to them suffering more abuse from both Sonic and Robotnik. Grounder's dopey, puppy eyed disposition doesn't help.
Robotnik himself comes dangerously close at times, especially in episodes involving his mother.
I just love sharing a cozy, hot cup of lapsang souchong tea.
Moral Event Horizon: Although he is cartoonishly goofy, many, if not most of Robotnik's plans involved at best enslavement for life or at worst mass murder of civilians. For example, in "Sonic Gets Thrashed", his entire scheme revolves around killing his own robotic creations and enslaving many Mobian citizens.
Sonic could be seen as this as he sadistically tortures Robotnik, Scratch, Grounder, and Coconuts. Though it can be argued that they deserve it, and Sonic does it, as much for other bullied citizens, as for himself, they are so pathetic, people will feel bad for them regardless.
When Coconuts decides to run away and possibly be good, Sonic tells him to stay with Robotnik. His scheme in the pilot episode also seemed reliant on Sonic being as obnoxious a customer as possible.
Robotnik himself in some episodes ("Lovesick Sonic", "Robotnik Jr."), where the expressive animation makes him look like a big orange teddy bear.
They Wasted a Perfectly Good Character: The show had some decent one shot characters. Perhaps most blatantly were Robotnik's earlier bots who, despite being utilised and even given names and personalities in Dr Robotnik's Mean Bean Machine, made only cameos in the pilot and one or two more episodes if very lucky. The show also adapted Princess Sally for a voiceless cameo in the Christmas Special.
Usually Tails. Sonic also has his moments, such as the episode "Sloooowwww Going". It's even Lampshaded in this YouTube Poop. For all the Rooting for the Empire the show garners, it did like to offer hard reminders why they weren't supposed to lose.
Coconuts could be this when you realize he is actually trying to get a promotion instead of being evil.
Goopster the alien in "So Long Sucker" is quite The Woobie as well.