Robotnik's mother is incredibly abusive to him. In some cases, she almost makes him into a Jerkass Woobie.
This eventually carries over to Robotnik himself, who is also incredibly abusive to the robots he creates.
Acid Reflux Nightmare: The knowledge that Tails has these sometimes is what propels the resolution of an episode.
Achilles' Heel: In a more literal sense than usual: Robotnik falls into a vat of super-strength potion, and the only part that didn't hit was his... well, as he terms it, "caboose". Terms it after calling it his "unmentionable" two seconds before.
And That's Terrible: See above. "If someone tries to touch you in a place or in a way that makes you feel uncomfortable, that's no good!" Admittedly the show was aimed at kids generally under 10 who probably could use the warning.
When Sonic and Tails are pulled over (on foot) for speeding, Tails suggests they outrun the policeman before he takes them to court. Sonic replies, commenting on how that would be illegal.
Arson, Murder, and Jaywalking: "You lost my rocket ship, you let the hedgehog ruin my plans, and NOW YOU'RE RUNNING UP MY LONG DISTANCE BILL!" - Robotnik
In the episode "Super Special Sonic Search and Smash Squad", when listing Sonic's offenses, Robotnik tells his men that Sonic ruins his schemes, he escapes his traps, and he helps nice people.
From the episode, "Birth of a Salesman":
Robotnik:"Listen, Weasley, you are brash, arrogant, obnoxious, pushy, rude, and you dress funny. You're my kind of guy!"
Ascended Extra: Several background characters from the second (officially aired) pilot "Super Special Sonic Search and Smash Squad" are used as opponents in the Genesis video game Dr. Robotnik's Mean Bean Machine, being given slight redesigns and individual names and personalities most of them didn't even have long enough to establish in their one appearance in the show. Scratch, Grounder and Coconuts themselves come from badnik designs from Sonic the Hedgehog 2 (with Scratch being the most radical change).
Ass Kicks You: In "Zoobotnik", Mama Robotnik rams into Katella butt-first, leaving her flattened against the wall.
Attack of the 50-Foot Whatever: Tails in one episode. In the Chaos Emerald saga, the Supreme High Robotnik, Master of the Universe. As well the odd walker machines used by Scratch and Grounder which are basically cockpits attached to massive walking steel beams with overly massive shoes. Sonic panics when he sees some massive robots in The Last Resort, but before he has to fight them, they surrender and run away for no explainable reason. Also Scratch, Grounder, and Coconuts are caught in a huge explosion at the end of the episode Trail of The Missing Tails and become extremely huge.
Babysitting Episode: In the episode "Baby-Sitter Jitters", Sonic and Tails wind up babysitting a trio of baby beavers. Tails made the offer to the parents because Sonic "loves babes".
Bad Butt: This incarnation of Sonic is one. On one hand, he's supposed to be a cool character with attitude. On the other one, he delivers boring speeches and aesops to kids at the end of every episode in the infamous Sonic Says segments...
In another episode he practically turns into a parade float after eating a huge quantity of dehydrated food, then drinks a glass of water.
In the episode "Pseudo Sonic" Sonic ends up with this after he accidentally follows Pseudo Sonic into Poison Flower Valley, which has effects similar to poison ivy, causing Sonic to get extremely itchy, followed by making him bloat up like a balloon. He stays like that for pretty much the rest of the episode. Poor Sonic, he gets fat and stays like that once in a while.
Batman Gambit: Sonic frequently does these to Robotnik and his lackeys.
Beehive Hairdo: Parodied in "Momma Robotnik Returns", when a social worker has actual bees flying around it.
Beware the Silly Ones: How Mobius would fare if Sonic wasn't around to stop Robotnik's plans (or if Tails wasn't around to save the day whenever Robotnik, Scratch and Grounder actually succeeded in immobilizing Sonic) is surprisingly dubious for a show with Adventures of Sonic the Hedgehog's reputation for wacky comedy.
"Blind Idiot" Translation: In the American Spanish translation, Tails is translated as a female character. For Latin fans of the games, this created a series-long problem, especially when talking to people who only knew of Sonic via the Spanish translation of the cartoon, and of course, were entirely (and understandably) convinced of Tails's female gender.
Bond One-Liner: In one of the PSAs, when Scratch and Grounder get run over by a truck. "Looks like these dumbots were flat out wrong about going in the street!" Leads to a bit of a Broken Aesop as Sonic then spends the remainder of the PSA standing in the street.
Boobs of Steel: Katella the Intergalactic Huntress, one of the bustiest characters on the show and also one of the most aggressive. She has enough strength to break down a door and make a badass entrance.
Bound and Gagged: Many characters, including Sonic and Tails, end up like this a lot.
Broken Aesop: Quite prone to this, since it tries to shoehorn Aesops in while being slapstick.
An episode about the importance of reserving 911 for emergencies is broken by Sonic using two robots attempting to kill him as an example of what NOT to waste 911's time with. Sonic can defeat them fairly easily, but "don't call 911 if you think you can probably handle the life threatening situation" isn't nearly so great a message for helpless kids.
Brilliant, but Lazy: A very good case can be made for Robotnik falling into this trope. In the episode "Birth of a Salesman", Wes Weasley sells him a variety of weapons that are surefire tools to catching Sonic, yet Robotnik passes them all off to Scratch and Grounder, who of course fail miserably, being too dumb to use the gadgets properly. Oddly enough, Robotnik puts most of the blame on Weasley, demanding refunds and accusing him of selling defective products. Weasley points out that if anything, his gadgets have worked too well, and are in incompetent hands. Robotnik remedies this by...threatening Wes Weasley into going along with Scratch and Grounder to oversee Sonic's capture, despite clearly being the only one capable of effectively operating the weapons, or at least more capable than his minions "supervised" by an unwilling peddler. The good doctor doesn't seem to realize capturing his hated enemy may require physical effort on his part. You'd think he would either step up his game or quit whining.
Brother-Sister Incest: Breezy and Robotnik Jr. Being robots, this is easy to miss, but it's not helped by the fact that "Hero of the Year" gives Breezy's full name as "Miss Breezy Hedgebot Robotnik".
Butt Monkey: Pretty much all of the bad guys, but especially Coconuts.
Clueless Aesop: The Sonic Says segments were absolutely drowning in these.
The first episode's Sonic Says segment showed Sonic and Tails surrounded by Badniks. Tails suggests they call 911 and Sonic tells him not to do that unless it's a real emergency. Although Sonic is very capable of trashing an army of Badniks, children could very easily get the wrong impression and think that Good Old Fisticuffs is the right approach when surrounded by bigger, stronger, and possibly armed attackers.* Actually, fighting in self-defense may seem to be the right approach when you have no time to reach for a phone or cellphone by the time stronger foes quickly approach to kill you, or if the power is out when trying to use a phone. Possibly, the writers themselves realized that this was a stupid lesson to teach kids, so in a later Sonic Says, Tails is being chased by Badniks, and calls for help by a nearby police officer. He arrests the Badniks, and Sonic congratulates Tails for doing the right thing.
Another one has Sonic talking about how bad an idea running away from home is. This one is fine in itself, but he was telling it to Coconuts, whose "parent" is Dr.IvoRrrrrobotnik.
Sonic begins the "Poison Ivy" Sonic Says by saying "There may not be any poisonous flowers on Earth." ┐Que?
Conviction by Contradiction: In one episode Sonic's special sneakers are stolen. Sonic dismisses one suspect because his feet are too big to wear them, but the guy who actually stole the sneakers didn't want to wear them either. In fact, none of the suspects did.
Determinator: Even on the rare occasion he is faced with a genuine threat, Sonic is never one to give up.
Disguised in Drag: Sonic does this all the time, in addition to putting on ordinary male disguises. Despite always being obviously in disguise, Robotnik and his cronies never seem to be able to tell it's him, with a few small exceptions.
Slightly lampshaded in one episode where Sonic dresses up in a red dress, fruit hat, and lipstick to do something "really funny and cool" to Scratch and Grounder, but decides against because the two of them are already engaged in silly bickering over Grounder's nose of all things.
In one episode, Grounder makes a comment on the radio about being "single and willing to disassemble". Now think about what that would mean for robots.
Also, the rivalry among Robotnik's robots seems to be a reference to sibling rivalry. "He made me first! I'm his favorite!"
Scratch really goes to town with that plunger of his in the opener. He's got his tongue hanging out and everything!
The Dog Bites Back: Scratch and Grounder are usually mindlessly loyal to Robotnik and recessive to his constant abuse. They are shown to exploit the odd moment to get revenge on him however (with varied success).
Double Standard: Abuse, Female on Male: Subverted. In "Zoobotnik" intergalactic huntress Katella falls in love with Robotnik, but she absolutely refuses to keep her hands off him. Robotnik doesn't love her but he's too scared to say anything, and is visibly relieved when Mama Robotnik shows up and interrupts their Shotgun Wedding, whereby Katella calls off the whole thing because she refuses to have Mama Robotnik as an in-law. Sonic himself was the one who invited Mama Robotnik, but it was more to get rid of Katella than for Robotnik's sake, though Katella's abuse was not considered a good thing.
Even Evil Has Standards: Dr. Robotnik was disturbed enough by his loony cousin Dr. Warpnik that he banished him to the Warp of Confusion just to keep the dangerous fish-obsessed loon away from Mobius.
While not a villain per se, Wes Weasley is willing to aid villainous causes if paid enough. But even he wouldn't vote for a tyrant like Dr. Robotnik when he runs for office. Of course, that's quickly subverted when Robotnik shows him the payload he'll get for helping him.
Exact Eavesdropping: In one episode, Sonic is trying to figure out Robotnik's plan, who then proudly recites his plan to himself next to an open window.
Exit, Pursued by a Bear: One episode ends with Robotnik being chased by the slime monster from the space station Sonic and Tails were on. Another ends with him chased by an alligator.
Wes Weasley is very clearly inspired by Phil Silvers.
Scratch and Grounder also seem like evil but dimwitted versions of C-3PO and R2-D2. There's Scratch, the tall and bossy robot, and Grounder, the stout Swiss Army-bot. On the flipside, they seem to form a Fountain of Expies, as other Sonic media tends to give Robotnik/Eggman Those Two Bad Guys as his dimwitted right-hand men.
Expressive Mask: In "Magnificent Sonic" Scratch uses a mask in the shape of a mustached man with a moving mouth in order to deceive Ms. Possum.
Every Man Has His Price: Robotnik almost quotes the trope by name when offering Professor von Schlemmer diamonds in exchange for converting his "Dream Machine" into a "Nightmare Machine". Von Schlemmer instinctively accepts, but then reconsiders.
Family-Friendly Firearms: "Magnificent Sonic" in spades. Even the "Sonic Sez" that warns about the dangers of guns plays this straight.
Fan Disservice: There's many shirtless shots of Robotnik, as well as scenes that draw a little too much attention to his rear end. The epitome of this trope, however, is that bikini shot in "Hero of the Year." Seriously, are all those scenes of Robotnik bathing/shirtless/in skimpy clothes/wriggling his butt really necessary?
What makes this all the more hilarious is how in an interview, Milton Knight (the show's head animator) mentions that in creating Robotnik's design for the show, he strove to convey the doctor's perception of his own sexiness. It's no wonder he calls Robotnik "animation's sexiest fat man." and why Robotnik-in-bikini is in the page picture of Fan Disservice.
Fantastic Aesop: One episode has Tails disobey the "No Flying" sign and Sonic heavily scolds him for it, and at the Sonic Sez at the end, Tails even has to go to the juvenile office for it. The moral is supposed to be "obey every law". We see quite a few avian characters throughout the show (hell, the judge in that episode is an owl), so the law probably applies to them as well.
Felony Misdemeanor: Robotnik's quip against Sonic in the episode "Super Special Sonic Search and Smash Squad":
Follow the Leader: The abstract, Jackson Pollack-esque backgrounds? The thin, nonsensical plots? The loose, Off Model animation? Yeah, a lot of this show was, shall we say, inspired by The Ren & Stimpy Show. Justified in that a number of ex-Ren & Stimpy crew members actually worked on the show.
'Tiny Toons Adventures and Animaniacs may have had some influence on this show, considering that the animation company TMS actually did work on all of those shows as well as Adventures of Sonic the Hedgehog''.
Fountain of Youth: Sonic, Tails, and Dr. Robotnik get turned into babies in "Musta Been a Beautiful Baby". Hilarity Ensues.
Friendly Enemy: Scratch, Grounder and Coconuts come across as being on better terms with Sonic and Tails in some of the "Sonic Sez" segments.
From Bad to Worse: Coconuts tells Robotnik about the dream machine, but gets yelled at for not stealing it. Coconuts catches Tails, and gets demoted because it's not Sonic. Coconuts warns Robotnik that Sonic said he'll outsmart him, Robotnik takes it out on Coconuts and essentially demotes him as far as he can go. Each time it seems Coconuts falls farther and farther (literally).
Sonic dupes Robotnik into trading loot he stole from a nearby town for fake gold. Coconuts gets blamed in spite of not even being around for the dupe.
Fun with Acronyms: In the episode, "Robotnik's Rival", D.U.F.U.S., Dr. Quark's robot, stands for Design Unit Flexible Underling Substitute.
Oddly, her moustache appears during her second appearance, but was present in ever other appearance she made in the show.
Giving Someone the Pointer Finger: Robotnik in "Super Special Sonic Search and Smash Squad" and "Big Daddy". In the latter episode, said pointer finger was drawn big enough to take up a good portion of the screen.
Go Karting with Bowser: Some of the "Sonic Sez" segments involve Sonic trying to give advice to Robotnik's mooks (with varying success).
Heroic Sacrifice: In Tails' Tale", Sonic brings LeQuack and Tails to safety from a cursed temple at the expense of having to remain prisoner in said temple. However, this convinces King Kommamachs that Sonic's not as evil as Robotnik led him to believe.
High-Class Glass: Grounder gets one in the aforementioned "Grounder the Genius".
Humiliation Conga: Happens to Robotnik in nearly every episode. Particularly noteworthy is the ending of "Robotnik Express" and "Robotnikland".
I Am Not Weasel: Quark, who, despite his duck-like lower half, insists that "I'm not a duck!"
Ice-Cream Koan: Master Kwai Chang Crane perpetually rode the line on this. Some of his statements were alarmingly sensible.
"Surprises along the path of life are like dirty socks in the laundry of barefoot cousins."
If I Wanted You Dead...: In one episode, Tails had been kidnapped and Sonic thought it was Robotnik's doing. Robotnik denied it by claiming he'd be torturing Tails had he kidnapped him.
I Have Your Wife: In order to get on "Lifestyles of the Very Good", Robotnik kidnaps host Throbbin' Screech's niece and threatens to drop her in lava. Screech acquiesces, although not without some consideration.
Impact Silhouette: Used to comedic effect in Pseudo Sonic in that while piloting the robot Tails had no way to go through doors other than bashing through them.
In Name Only: The actual stories told definitely don't have much to do with the games, and while the show borrows more elements from the games than Creator/DiC's other Sonic shows do, the trope applies to about everything present: Badniks appear in the series, but as wild variations from their game designs. Completely reinterpreted versions of actual Zones from the games are featured in the occasional odd episode; "Submerged Sonic" takes place in Labyrinth Zone, "High Stakes Sonic" takes place in Casino Night Zone, and "Trail of the Missing Tails" features the Warp of Confusion as a tribute to the Special Zones. There's a short story arc that deals with the Chaos Emeralds, but of course, they look and work completely differently from their game counterparts, not even getting the number of emeralds "right".
Interspecies Romance: Even though they're both robots, Robotnik Jr. (human) is involved with Breezie (hedgehog).
Landslide Election: Occurs at the end of "Sonic Is Running". Not even Scratch and Grounder or Mama Robotnik vote for Robotnik, since the former forgot to vote at all and the latter was so disgusted by her son's campaign that she actually voted for Sonic.
Large Ham: Robotnik, thanks in no small part to the incomparable Long John Baldry.
Robotnik actually invokes this in "Coachnik"; one of the ingredients he uses to create the titular Coachnik robot is "300 pounds of ham".
Laser-Guided Karma: In the episode "Sonic Brakeout" where Robotnik imprisoned a cartoonist for comparing him to Humpty Dumpty, Robotnik ended up falling in the same position as Dumpty (albeit not broken) and unable to get up on his own.
Letting the Air out of the Band: In "Sonic the Matchmaker", Robotnik, wanting a wife, puffs out his chest and claims, "Any woman on Mobius would be proud to be 'Mrs. Robotnik'". The music dies as Scratch and Grounder look skeptically at each other.
Leitmotif: Several of of the recurring characters have music that plays alongside their scenes. Most recognizable is Sonic's, which doubles as the show's title theme. Robotnik also gets a pretty catchy one. Even Scratch & Grounder have one, which is just a shortened version of Dovregubbens Hall.
Mistreatment-Induced Betrayal: The reason why Robotnik's plan fails in "Hero of the Year"; Wes Weasley helps Sonic escape from his prison as a result of not being allowed to broadcast his shopping channel.
Mythology Gag: Despite being named Robotnik as opposed to Eggman, Robotnik makes a very, very large amount of references to eggs, either in puns or in his general planning (like the Omeletta episode noted above), in reference to his alter-ego; in the beginning of "Robotnikland", he even flies into a rage when Scratch and Grounder attempt to serve him pancakes for breakfast, rather than the egg-related dishes he prefers.
The episode "Lifestyles of the Sick and Twisted" actually had Tails call Robotnik "Eggman".
A cartoonist drew a story featuring Robotnik as Humpty Dumpty.
One episode has Sonic find a tunnel full of rings.
The unaired pilot episode contains several references to the games which includes the Egg Mobile-H from the original Sonic the Hedgehog and some of the Badniks from Sonic the Hedgehog 2.
The scene in the end credits originated from the pilot.
Near Villain Victory: Robotnik did actually come very close to defeating Sonic a fair few times. He does so each time he gains a Chaos Emerald in the four parter arc, only for Sonic to usually manipulate some time paradox against him.
Never Say "Die": The show went to great lengths to avoid this, with "Road Hog" being an exception.
Nice Hat: Most of the characters have worn some of these during the show.
No Indoor Voice: Dr. Robotnik has a penchant for being loud and boisterous.
Not Me This Time: One episode featured Tails being kidnapped and it wasn't Robotnik's doing. In another episode, somebody steals Sonic's shoes. The fact Coconuts had been caught at the crime scene suggested he had something to do it but Sonic reasoned Coconuts would have captured him instead of just stealing his shoes.
Once per Episode: Robotnik's catchphrase "I hate that hedgehog!" which is generally said at the end of most episodes. Played with in "Over the Hill Hero," where, shortly after Robotnik has retreated with his mooks, Captain Rescue ends the episode with "I like that hedgehog!"
Wes also says "I love that hedgehog" at the end of "Hero of the Year".
There are a few episodes where Robotnik does not say the phrase once, including the above-mentioned "Over the Hill Hero".
Paper-Thin Disguise: Sonic is a master at this. It happens in almost every episode, and Scratch and Grounder fall for it every time. However, there were occasions where Sonic and/or Tails fell for these as well.
Taken for Granite: Used four times throughout the series: first by Grounder in "Grounder the Genius", then by Scratch and Grounder in "Tails in Charge", then by Coconuts in the episode "The Magic Hassle", and last by Merlynx in "Hedgehog of the Hound Table", though that time it only affected Sonic's legs.
Terrible Trio: Scratch and Grounder with Robotnik as the higher up. Sometimes Robotnik himself joined them, and led from the front. Semi recurrer Coconuts also joined the team on occasion.
That Came Out Wrong: In "Sonically Ever After" Sonic and Tails first end up in the story of Hansel and Gretel. Upon noticing he's been hampered with the latter role, Tails points out "Hey, I just noticed; I'm a girl!". Doesn't help that a handful of fans have probably mistook him for one in the past.
Theme Tune Cameo: Catty Carlyle's song in "Sonic's Song" is the show's theme song With Lyrics. The theme song also uses portions of "In the Hall of the Mountain King" and "Flight of the Bumblebee". Both of these (along with certain background tunes) also take elements from the title theme for Sonic 1 and 2 for the Genesis.
Timey-Wimey Ball: Sonic and Tails defeat Robotnik in several different eras, keeping the Chaos Emeralds out of his hands. Robotnik, in a rare flash of ingenuity, goes back to the time periods and grabs the Emeralds anyway. Sonic and Tails defeat him by traveling through time to the same timeuntil about a dozen temporal clones of each have assembled, totally smashing any pretense of a Stable Time Loop in the process. The fact that it toys with so many time travel tropes is one reason this four-parter is well-regarded.
The second attempt, which is sung very badly by Robotnik himself, actually becomes Hilarious in Hindsight (and a tad ironic), considering that his voice actor Long John Baldry was a professional blues singer.
Vocal Evolution: If you watch some of the earliest Adventures Of Sonic The Hedgehog episodes, you'll notice that Scratch and Grounder talk quite differently from their later performances ´┐Ż Scratch is voiced with a Brooklyn accent, whereas Grounder has a lower, stupider voice. These attributes disappeared over the course of the series. (Grounder still sounded dumb, but less so.)
An odd case in the German dub: Gerald Paradies and Oliver Feld had already adopted voices for the henchbots right from the get-go (Paradies adopting a nasally voice and Feld an appropriately chicken-y voice), but for some reason, during the flashback in the first episode where Robotnik is shown making Scratch, Feld's voice for Scratch was a rather cute variation of his normal speaking voice (up to the line "Mein zwillingsbruder? Bin ich so haesslisch?!"); then when he first interacts with Grounder, Feld switches back to the previous voice. Paradies' Grounder also got slightly higher over the episodes.
Volumetric Mouth: When Grounder's head lands on Robotnik's foot in "Grounder the Genius", it results in Robotnik's mouth briefly becoming as large as his body.
Walking the Earth: Pretty much what Sonic and Tails do for the entire series because they are never sure where Robotnik will strike next.
William Telling: Sonic does this to one of Robotnik's robots. Getting up in Robin Hood garb and balancing an apple on his head, Sonic tauntingly asks the robot (Called Dragon Breath in Dr. Robotnik's Mean Bean Machine) if he's ever heard of William Tell. Infuriated, Dragon Breath throws his spiked club at Sonic, but the hedgehog's super speeds allows him to dodge just in time, so that the only damage done is that apple is split in half...and the tree behind Sonic falls over onto Dragon Breath.
With Friends Like These...: Sonic delivers a variant of this in "Over The Hill Hero" to Captain Rescue for cutting in on his heroism.
You Answered Your Own Question: "What would I want with a two-ton baby ape who can lift giant rocks, fire bananas like a shotgun— HUH? and help me capture that pesky hedgehog SO ROBOTNIK WILL TAKE ME BACK!"
YouTube Poop: A frequently used source, if only for the sheer number of ways that Robotnik can be made to say 'penis' and other swears.