Aborted Arc: A small character arc involved Bocoe and Decoe getting sick of Robotnik's evil crap and doing a Heel-Face Turn, aligning themselves with Sonic and his friends. The episode after this suitibly showed the two living at the Thorndyke mansion with the rest of the gang and helping out around the house. After that episode, this was pretty much abandoned for no clear reason. The closest thing to an explanation was a line or two somewhat implying that Robotnik convinced them to come back.
Aloof Ally: A rare case that is also the main hero. Sonic, though a lot friendlier than regular examples, usually keeps to himself, and doesn't get into the action until the situation truly becomes dire.
Animation Bump: The first few episodes have noticably smoother, more expressive and consistently on-model animation compared to later on.
The season finales and the last episode or so of every adaptation arc also had this.
Starting with the second season, scenes involving machines used rendered animations with cel shading, which upped the graphic quality immensely.
Anti-Villain: Dr. Eggman. Arguably more an Affably Evil villain early on, but by the third season, his role as true villain is all but gone.
Affably Evil: Dr. Eggman is perhaps the most kind-hearted evil tyrant around. The 'evil' part is nearly non-existant by the end of the show's run.
Antagonist in Mourning: When Sonic seems to be gone for good in "A New Start," Eggman takes the Egg Fort to the skies loudly and obnoxiously trying to find him, ostensibly so he can finally make sure he's dead and start his empire safely. When Sonic returns, Eggman is notably ecstatic even though he had just been thoroughly defeated, and gleefully goes off to plot his revenge, laughing all the way.
Ash-Face: This happens to various characters at various times, usually whenever Bokkun delivers a (self-destructing) message/bomb
Asleep for Days: Sonic after fighting Dark Oak for the first time, according to Eggman (in the dub, at least; he originally didn't specify how long Sonic had been lying there). He did take a plunge from the planet's upper atmosphere, after all.
As Long as It Sounds Foreign: If it wasn't important to the plot, signs in the background would have arbitrary Roman Letters written on them. They didn't even try to make them spell anything meaningful.
Big "NO!": Chris' reaction when the Eggsterminator kicks Sonic into the water after delivering to him a No-Holds-Barred Beatdown, which Eggman tried to get it to stop doing.
Cosmo does this too in the original version when she remembers the time that Dark Oak called her "White Seed" before her escape from her sisters' and mother's exploding starship at the end of the sixth-to-last episode.
Break the Cutie: That's what happens when you make Tails execute the girl he loves.
Breaking the Fourth Wall: Not much in the dub, but plenty in the original, though even so much more frequently in the beginning of the show than towards the end. For example, in "Cruise Blues", Decoe and Bocoe explain that it took them two weeks to repair the EggFort because they weren't in the previous episode, though in the dub, it's because Decoe kept complaining. Also, after the EggFort 2's (very far away) transformation, Eggman gets calls from Sonic X viewers saying that they couldn't see it. Eggman then tells them to get bigger TVs. (This was changed in the dub to someone complaining through the phone that the EggFort 2 "isn't all that", and Eggman exclaims, "I'm getting an unlisted number!")
From the dub: "Kids, don't use Formula One race-cars to catch hedgehogs!"
In the dub of the episode where Eggman blocks out the sun and "helps" people by giving them Solar Balls, when Eggman starts fantasizing about what it'd be like if he had his own TV show called "Eggman X." He even announces to the audience to stay tuned for next week's installment.
In the sub of episode 10, during the baseball game against Eggman, Sonic catches a home run ball outside the fence and is told by Chuck that it's against the rules.
Sonic: "Why do we have to play by the rules now? This is an anime."
Another one that made it into the dub, in "Countdown To Chaos" the military attacks Eggman with tanks copied off of his designs. As he rants about it, Decoe cheerfully holds up pictures of the robots in question from previous episodes for the audience.
The first episode that features the Chaotix Crew has them introduce themselves to the camera.
Bring It: A couple of times, Sonic insults Eggman (or one of his mechs) by turning his back and smacking his own bottom.
But Now I Must Go: The first series finale, where our heroes have finally built a portal that will send them all home. But then Chris, in a moment which did not at all help his already shaky status in the fan-base pulls the plug on it before Sonic can get through. They say goodbye properly at the end of the episode and it's (surprisingly) poignant, seeing as the fact that we never actually see Sonic disappear, as well as the revelation that Sonic could have gotten home whenever he wanted to, but chose to stay with Chris.
Butt Monkey: Knuckles gets this a lot in later episodes, as do the Chaotix in most of their few appearances. Eggman and his cronies also often play this role in a villainous sense.
Members of Chaotix even become Butt Monkeys to each other.
Charmy: "Ladies and gentlemen, welcome to another episode of Delusional Thinking With Vector! Just look at him go, ladies and gentlemen, he's out of control! There's no stopping him!"
The Cameo: Episode 48 features a Lost World where Chris, Decoe, and Bocoe are briefly chased by (a somewhat smaller and more bestial version of) Mothra, and later on the cast is attacked by Mogera, who chases Eggman, his 'bots, and Chris around before facing off against Sonic, Knuckles, and Rouge. A statue of Godzilla also makes a brief appearance.
Collapsed Mid Speech: Sonic in episode 54 likely due to a combination of exhaustion and an arm injury.
Combining Mecha: Decoe and Bocoe, although the first occasion of this happening was subverted. Also, Eggman's ship, the EggFort 2, was actually three separate creations that also combine into the Eggsterminator (E-99 Egg Emperor), although the actual combination to the EggFort 2 was ridiculously zoomed out.
Some of the Chaotix's treatment leaned towards this too. The occasion they attempted to come on board the Blue Typhoon happened to be the one occasion the heroes decided to attack an alien intruder unprovoked, unarmed or even without the knowledge they were actually Metarex (though granted they felt kinda bad about this when they figured it out).
The Comically Serious: Easily the most obvious reason Knuckles is something of a Butt Monkey. You can literally gauge how badly a scene will go for him based on how humorless or stiffly he acts before things go south.
Comic Book Time: The series lasts chronologically long enough for characters to have at least aged a year, as such the series avoids the issue of ages in the Meterex arc, being no longer shown on eyecatches.
The Complainer Is Always Wrong: This seemed to become a running gag—a recurring situation would come in which Knuckles would object to a team mission plan, usually leading the gang to use peer pressure and goad his ego and bravery until he gave in. In the Metarex arc they instead just physically threatened him. Also led to Moral Dissonance since the gang also spent a lot of time explaining to Knuckles how he shouldn't constantly fall for Eggman manipulating or tricking him into working for him.
In Episode 57, Knuckles' arguing with the others (once again warning of how Eggman abuses him) leads to a planet egg getting stolen; he attempts to retrieve it but it turns out the one he collected was a fake, with Sonic and Chris using Knuckles as a distraction while they protect the real thing. After Knuckles is shown to be humiliated by this they give him a somewhat condescending pat on the back, the basic moral seeming to be, "You're better off being a patsy for us than thinking stupid ideas yourself." Ironically the dub subverted this somewhat in this scene, in which Cosmo comforts Knuckles (humiliated about Eggman using him) claiming he only believes the doctor's lies because he believes in peace and that anyone is capable of good.
Conspicuous CGI: The X-Cyclone would often appear as a highly-detailed and rather realistically shaded CGI model for shots that didn't have the characters in the cockpits or standing on its hull visible, and several times with traditionally-animated vehicles in the same scene. The Egg Carrier was also rendered in CGI in most of its appearances, but it was toon-shaded to closer resemble the traditional animation.
Curbstomp Battle: Super Sonic dished these out frequently (most notably against Perfect Chaos). Dark Oak made his malace known by being the one Worthy Opponent Sonic's super form had in the anime.
And then Cosmo, who had until then been practically useless in a fight, takes him out.
Curbstomp Cushion: A bad guy variant by Eggman was often the nearest he had to proving his worth against Sonic. He could knock Sonic down a few times, but the latter usually quickly recovered and quickly left the doctor's mech of the week in scraps.
Arguably Shadow vs Knuckles, the former very quickly leaves the latter on the floor two bouts in a row, however within that time Knuckles is able to throw Shadow's rolling form smack into a wall. The second scuffle also drains Shadow to the point he nearly faints from exhaustion (oddly 4Kids cuts out this scene making it more on par with a Curbstomp Battle).
Deliberately Cute Child: Cream, though usually genuinely innocent, is suggested to exploit this trait a couple odd occasions, perhaps most triumphantly against one of Eggman's sentient mooks in a baseball game.
In the game adaptations, the Egg Viper, the final boss of Sonic's story and one of the most popular boss battles of the series, has about one minute of screen time, while the Egg Walker, Tails' final boss battle, doesn't even appear. Egg Golem and Biolizard similarly have little to do other than show up, be menacing, and wander off/die.
Also, in episode 1, Sonic jumps on top of an S-Team race car during a chase, causing the driver to protest that they don't want any kids copying him. In the Japanese version, Sonic duly warns the kids in the audience never to stand on moving cars. The dub parodies this: Sonic instead tells them not to chase hedgehogs with F-1 race cars.
Dramedy: The series sinewaves between slapstick, almost Looney Tunes-style comedy and dead-serious, somber sequences.
Dub-Induced Plot Hole: In Episode 16, Chris twice holds up a sign telling good kids not to attempt his latest scheme. Sonic also holds up a sign sarcastically asking if he's saying Sonic isn't a good kid. 4Kids blanked out the signs, making it look very awkward as Sonic and Chris are standing there holding up blank signs to the audience. Okay, so it's not really a plot hole, but it's still really stupid for a dub.
There are plenty of these throughout the series, for instance, 4Kids blanking out Vector's name on the handkerchief that Tails picks up in a series 3 episode (itself a scheme to try to hook Cosmo up with Tails by having him pick her handkerchief up, a plot point 4Kids also cut out.)
The blank signs are probably the fault of TMS (the animators), rather than 4Kids. They're known to "pre-airbrush" their other anime too.
This "airbrushing" was once done rather reasonably. In one episode an Artifact of Doom had a crescent moon and star on it in the Japanese dub, but the star was gone when broadcast in English because the crescent moon and star is a common symbol and Islam. It was done to avoid offending anybody.
Ensemble Darkhorse: In-Universe example with Knuckles, despite his frequent role as the team's Butt Monkey and embitterment about Sonic's endless popularity, he is in fact revealed to have a large base of fans around the world (something the others exploit to coax him into a promotional Battle Tournament).
Even Evil Has Standards: From the 4Kids dub: "It's one thing to take them prisoner and threaten them but when you actually hurt somebody, that's going too far".
Exiled from Continuity: Despite being very similar to the games in story and characterization, specific elements created for the series are not allowed to be used in other Sonic continuities due to copyright issues. The closest exception was a cameo of the series promo art in an optional side quest in Sonic Adventure DX, and a brief crossover between this series Sonic X and Archie's Sonic comic (the former being a series that was given a legally mandated embargo on using elements from several Sonic series, including Sonic X, and an event that is likely the reason why Sega will not allow Archie to reprint their Sonic X comics).
Eye Catch: Cut out from the 4Kids dub, but surprisingly left in the references to them in the Chaotix's debut episode.
Eyelid Pull Taunt: Sonic does this once while standing on the arm of one of Eggman's mechs in order to goad it into hitting itself. This was cut from the 4Kids dub (though Vortexx does notably showcase it in one of their commerical bumpers).
Falling Into His Arms: Happens on a few occasions with Chris and at least once or twice with Amy, Cream, and Cosmo.
Family-Friendly Firearms: In the 4Kids dub, the guns fire lasers instead of bullets. The strangest thing is, they still look EXACTLY like guns; the sound effects were just altered.
Except the dub also left in the bullet casings being ejected.
On occasion, this actually made more sense than the Japanese sound effects however. In a reverse situation to the dub for example, E-102 Gamma's laser fire makes bullet fire noises in certain episodes of the original edit, while the dub sounds more accurate with it's usual laser noises.
Eggman, at least in the English dub. Initially a goofy yet still formidable Affably Evil villain, he became more bumbling and good natured to the point of giving fellow villains lectures about being merciful to their captives.
Amy started off as a genuinely high-spirited and kind-natured girl with occasional Tsunderemood swings. This element of her persona eclipsed her character until she became a brattyBitch in Sheep's Clothing that the cast was either irritated by or outright terrified of.
It is perhaps worth noting that most of these cases mirror the evolutions of their games counterparts at the time, albeit Up to Eleven.
Foreshadowing: In the first season finale of the dub, we get this exchange, which gains a bit more impact when you realize this show later featured an adaptation of Sonic Adventure 2.
*Eggman uses a more powerful than average explosive*
Bocoe: One of these days you're going to blow up the whole planet.
Eggman: It's a distinct possibility.
Also, in one of the last episodes:
Chris:And if he [Sonic] can save it, we can too! Right, Cosmo?
(Cosmo is silent.)
Freeze Sneeze: Sonic does this after jumping into the ocean to save Amy presumably due to getting soaked.
Friendship Denial: In a couple of episodes of the first season, especially in "Cracking Knuckles", Knuckles would blatantly deny being friends with Sonic, but this is due to his irritation of Sonic's attitude and recklessness.
Genre Savvy: The Chaotix, despite their occasional incompetence, are very savvy. It's even more prominent in the Japanese version, where they constantly break the fourth wall.
Espio: Change the scene and suddenly you know where Sonic is. Is it just because the program's almost over?
Getting Crap Past the Radar: Several moments when Rouge flirts with Knuckles: "I hope you're active at night..." and "I hope we share a cell together..." come to mind...
Similarly, in the dub, concepts like love are considered inappropriate for American children, but having Rouge pull a locket out of her cleavage is A-okay.
Giant Space Flea from Nowhere: E-105 Zeta. In Sonic Adventure, he appears about as early as during E-102 Gamma's mission to capture Froggy. In the anime, he doesn't appear until Gamma goes to the Hot Shelter in "Revenge of the Robot", and even then Zeta's appearance was too brief to make any lasting impressions.
Harmless Villain: Eggman as time passed became less and less effective as a villain (though granted Sonic's own Invincible Hero qualities didn't help). Curiously, however, the doctor had Laser-Guided Karma on his side and his savviness and competance increased much more on the odd occasion he was working on the side of good.
Hero with Bad Publicity: For the first several episodes of Season One, Sonic and his pals were on the run from the authorities and spent most of their time hiding out in Chris's house when not foiling Eggman's latest scheme.
Heroic BSOD: Cosmo shows an interesting case near the end of Season Three. In the sixth-to-last episode, "Shadow's Arrival" / "The Cosmo Conspiracy", Dark Oak congratulates her for a job well done in helping him collect all the Chaos Emeralds at the end of the episode, that while calling her by her codename of "White Seed" that he gave her just before her escape from her sister's starship before its destruction. This causes Cosmo to remember the time that Dark Oak gave her the codename of White Seed, right before letting loose her Big "NO!" (in the dub, she just let loose a wailing scream). And then, in "The Lost Planet" / "Eye Spy", Cosmo is tossing and turning in bed in frustration with tears in her eyes knowing that she was secretly working as an unwilling spy for the Metarex, refusing to be anybody's friend just because of said knowledge and telling everybody to stay away from her. Before she can go to confront Dark Oak alone, she is stopped by Tails, and it takes his kind words and that of everyone else together for her to get better.
Heroic Sacrifice: Cosmo performs this in the second-to-last episode of the second series to help Sonic and friends defeat Dark Oak.
I Ain't Got Time to Bleed: Sonic in episode 53 was comatose for a week in Eggman's base after a fight with Dark Oak and has a wound on his upper arm throughout the entirety of the episode. He hardly ever pays attention to it until Knuckles points it out to him.
I Warned You: Often issued to Knuckles each time his truce with Eggman turns out to be a trick. Interestingly Knuckles never uses the trope the several occasions the team's plans go haywire (as he sometimes predicts, and is ignored), something that can be considered somewhat out of character for him.
Invincible Hero: Sonic on occasion really leans into this trope. The majority of times he beats Eggman and other villains rather handily and generally treats the whole thing as a fun little game. Shadow leans even further into this (and it's villainous twin earlier on) Sonic at least had problems with the Meterax, even in his Super form, Shadow on the other hand beat an entire army of them in one swoop.
Knight of Cerebus: The Meterax, especially Dark Oak, are established as much more demonic and powerful villains Sonic has ever faced before, giving the usually untrouncable hero a hard time even in his super form (that said their validity into this trope ranges due to individual armies and members having different lengths of evil, ranging from Laughably Evil Yellow Zelkova to emotionless like Pale Bay Leaf to even the Tragic VillainMagnificent Bastard Dark Oak himself).
For a more specific example, they in fact had to cut down Sonic's animation design. In the games he always has six quills on his back, which got reduced to only three in the show. For the most part it works, because that's all we usually see in his portrait view, but it's apparent when they have to show his backside.
An arguable case of Woolseyism in the dub, in the Japanese edit this non-sensical mechanism is activated due to a lack of ammo (though ironically the Japanese edit of the parade is actually cheering "Welcome").
Lonely Rich Kid: Chris claimed to be this, but it was noted by many that he does have genuine human friends; they just happen to be a small, close circle.
Love Redeems: Following Cosmo's sacrifice, Luke/Lucas reappears, reformed and repentant, realizing the errors of his ways as Dark Oak and the fact that his lust for power destroyed his own people and only brought pain and suffering to the universe. A vision of Hertia/Earthia appears before him and gives him a second chance, redeeming him, after which then he happily reunites with Hertia and they both depart for the afterlife.
Magic Skirt: Cosmo. Also Cream and Amy. Although Amy's skirt acts as if it might have a wire frame keeping it in place. A real thing, although unusual for skirts so short.
Mass Hypnosis: Eggman tries a particularly convoluted one of these.
Minion with an F in Evil: Decoe and Bocoe, despite being loyal to Eggman, are meek cowardly droids that resent some of their more callous orders from the doctor (in the anime's Sonic Adventure adaption for example, they are charged with disposing of the more incompetent E-100 Series models) and actually enjoy doing kindly deeds for people. They actually show enthusiasm when the doctor appears to turn a new leaf, only for it to usually be revealed as a another scam. That said it helped that by the final season Eggman himself had essentially became a Big BadWith An F In Evil.
Monster of the Week: The first 26 episodes used the show-exclusive E-Series robots in this role. Then we have the Metarex.
Mecha-Mooks: Decoe and Bocoe mostly cater to Eggman's every whim, while Bokkun acts as his messenger.
Men Don't Cry: When Sonic leaves Chris's world in the series one finale, you can tell that he's crying, you just can't see his eyes.
Mood Whiplash: Perhaps one of the most emphasised examples in most forms of Sonic media. Comparing the cartoony, harmless fun of the first few episodes to the somewhat grim finale certainly shows an uneasy shift in tone.
Mythology Gag: Chris's grandfather is an inventor named Chuck. In the oldcartoons and comic, Sonic had an uncle named Chuck, and Chuck was also an inventor. Sonic can also be seen eating a chili dog in one scene, his favourite food in the cartoons and comic.
Nobody Calls Me Chicken: Knuckles can often be swayed into a plan he initially shows disapproval or disinterest in by stroking or insulting his pride. At times this is exploited to ludicarous lengths by friends or foes alike.
Notzilla: Weasel using a flamethrower on a Godzilla lookalike.
Off Model: Hooooooo, boy. This is likely due to the series's limited budget.
Oh Crap: Eggman gets this quite often, like when he's about to get smacked for one more time by a pissed off Amy in Episode 9, and when his E-18 Guerra-Hard robot is about to explode after Sonic overpowers it thanks to the two Chaos Emeralds he snatched from it in Episode 13.
Only Sane Man: In the episodes "Sunblock Solution" and "Eggman for President," Eggman pulls a gambit to make people believe that his new "Egg Moon" has malfunctioned and blocking the sun, making himself a Villain with Good Publicity by producing Mirror Towers and Sunshine Balls to provide light while he fixes it. Sonic is the only person to realize right off the bat that Eggman is deliberately placing the Egg Moon in front of the sun because if it had really stopped in orbit, it would just stay in place while the Earth continued to move, but everyone thinks that Sonic has gone bad until he point-blanks tell everyone as such.
Panty Shot: Amy got a few of these. Or occasionally, a lack of them◊. It's actually surprising how many are snuck in there.
Cream gets one in the first Sonic Adventure episode, and also in one episode of the Metarex arc, when she was bringing some treats to the bridge of the Blue Typhoon. Surprisingly, this second one lasts for a good ten seconds, and was kept intact in the 4Kids dub.
Pinching Pain: Kani (A crab) just won't leave poor Sonic alone in episode 16. First it cuts his air hose when he's trying to find the emerald underwater then it clamps his tail rather painfully in it's claw.
Previously On: In the Japanese version of Episode 39, Charmy gets a Sonic X DVD, and Vector tries to play it on a film projector. Espio then "borrows" a DVD player from a convenience store and the Chaotix watch a montage of footage from the previous episodes. Perhaps because of the Moral Dissonance of Espio stealing a DVD player, this entire scene is cut from the dub, so a longer montage was added to the scene where Vector reads the newspaper to pad out the missing time.
"The Reason You Suck" Speech: Eggman gives this one out to Chris when he thinks he's lying about not being responsible for the world put to a time freeze.
Eggman: You're the one who's lying to yourself. You don't wanna accept the truth. Deep down, you know once Sonic is gone, your life will have to go back to the way it was before. Your days of adventure are at an end, boy, just like your friendship with that hyper-annoying hedgehog. All your dreams have been shattered, haven't they? Life is like that, kiddo. Take it from somebody who knows! Whenever you reach too high, life smacks you down! But on the bright side, at least you and I won't have to see each other ever again.
Retired Monster: Dark Oak at the finale of the second series where he finally realizes the errors of his ways after Sonic and co. defeat him with the Sonic Driver and help from Cosmo's Heroic Sacrifice.
Eggman: You figured out my scheme, kid. I despised Sonic so much I decided to bring time to a stand still. Then, I tricked this world's scientific expert into believing that Sonic had to be sent back. Now that you caught me out, confess.
Shipper on Deck: Amy is probably the one who made Cosmo realize she had feelings for Tails in the 3rd season when she remarks that the two seem cute together. Team Chaotix tries to actively ship the two in a later episode; though all of their attempts fail Tails and Cosmo still sort of get together on their own (it's never really absolutely official until Cosmo is killed).
Ship Tease: Sonic and Amy. Especially in the last episode of the first series, where Amy pours her heart out telling Sonic how she was ready to wait forever for him, and insists he admits he loves her. Sonic's reply is inaudible (in the Japanese version, at least, but judging by Amy's reaction, whatever he said, it wasn't "no").
The Egg-Fort 2 resembles the Enterprise from Star Trek.
In episode 39, Vector makes a spoof of Detective Conan by saying that he has "the brains of a genius and the appearance of a crocodile." He even has the glasses, hairstyle, and tone of voice to boot. Charmy remarks that he was watching the anime channel until morning.
The dub converts this to impersonations of Sherlock Holmes and Columbo (the similar jacket and mannerisms make the latter a rather swift transition).
Eggman's two-Chaos-Emerald-powered mecha is Mazinger Z.
From the same episode as E-90 Super Sweeper (aka Thunderbird 2), the launch sequence for the new X-Tornado (the collapsible palm trees) is also a shout-out to Thunderbird 2's launch sequence from the puppet series.
Mothra and MOGUERA appear in Episode 48 on a mysterious island. Mothra's a bit more vicious-looking and antagonistic (a nod to her dark twin Battra) and MOGUERA is based on his Showa appearance and battles Sonic, Knuckles and Rouge at the climax of the episode. Godzilla also appears as a statue that Bokkun sits on for a minute before it crumbles apart when MOGUERA appears.
Stock Footage: Very noticeable when Knuckles and Sonic first fight Chaos together. Also, the logo from the title is taken from a logo on the side of Sonic Advance's box.
The title card for "Chaotix' Electric Shock Love Tactics" uses silhouetted versions of official art for Tails (from Sonic Rush Adventure) and Cosmo.
Stop Drowning and Stand Up: When Sonic lands in a pond during a fight with Knuckles in episode 5, he instantly starts flailing and yelling in terror as if drowning. That is, until he realizes the water he's landed in is not even half a foot deep.
Bokkun:It wasn't me who put sleeping powder in your hot chocolate!
This Cannot Be!: Yellow Zelkova's reaction to seeing the columns that were obstructing the Blue Typhoon's path tumbling to the ground after Sonic and co. defeat him for the first time with the Sonic Driver, (which, of course, he survives, making him the first Metarex to survive a blast from the Sonic Driver itself) while at the same time beginning the trigger for the tumble of said columns.
This is also Amy's reaction to when Serpenter crushes her lucky bracelet made for Sonic by herself in a much earlier episode.
This Explains So Much: Sonic says this in Episode 74 after a hologram of Hertia/Earthia relates a story to Amy and Rouge about how Seedrius-Flora/Greengate got destroyed and how the Metarex were born.
This Is Not a Drill: In episode 33, when Dr. Eggman breaks into Prison Island, the following line is basically said by security.
This Is Unforgivable: In Episode 9, after Eggman's Serpenter robot crushes Amy's "good-luck" bracelet that she made for Sonic and makes her react to it with a variation of "This Cannot Be!", she cries over its breaking and then flies into a rage with fire in her eyes and shouts "Now you're gonna PAY!!!" before proceeding to charge at Serpenter, shout "Don't mess with me!", give Eggman an Oh Crap moment and pound the robot into submission and then go after Eggman himself, send him flying into the ocean, and then pound him one more time and then pass out and start sinking to the bottom of the ocean afterwards... only for Sonic to save her and recover and repair her bracelet.
This is also what Sonic himself says to Eggman at the end of the finale of the third season in the original version, which in the dub was replaced by the line of "Life never stays slow for long. Thank goodness! Watch out Eggman, I'm coming at ya full speed!"
This Loser Is You: A commonly accepted explanation for Chris Thorndyke's existence, is that he represents the target audience.
Believe it or not, Chris also took one in Season 3. Due to his mind being one of an adult he is now a talented inventor and strategist, capable of aiding the team.
Took a Level in Jerkass: Amy to an extent as the series progressed (the games version went through a similar evolution at this time though not to the same lengths). Also arguably a key reason for Chris' Scrappy status (though he swerves back in the Third Season).
While not nearly as consistently or to the same extent as the former examples, the show on occasion also liked to suggest a slightlydarkerhiddentint to Cream's persona compared to the games' version (which is usually just sweet through and through).
Theme Tune Cameo: In a few occasions, Eggman hums, and even SINGS, his leitmotif.
Through a Face Full of Fur: Tails blushes at one point when he carries Cosmo up to the ceiling by means of his helicopter tails in order to decorate a room for a party.
Tails blushes a lot during the latter half of season 3 around Cosmo, really.
Even if it's metal plating, Emerl fits this trope too in episode 46.
Tragic Keepsake: In the series finale, Tails recieves what's left of Cosmo in the form of a seed from Sonic after both he and Super Shadow attempted to save her with their Chaos Regeneration. Tails later cultivates this seed in a plant pot inside his workshop where at the very end of the episode it is seen sprouting.
Vitriolic Best Buds: Sonic and Knuckles at times. Knuckles and Amy often have this chemistry with a few team mates due to their brashness (especially each other).
Vocal Evolution: Decoe and Bocoe's voices in the dub initially are acted in a monotone Robo Speak. While the voices themselves remain the same for the most part, as the show progresses the acting for both gradually fluctuates to sound more emotional and human-like akin to their Japanese counterparts.
The cast for characters established for the games also slowly refine to sound more like the original games V As (though the difference would only really come to show in later games titles for which the 4Kids cast provided voices).
Not exactly evolution, but Cream's voice in the dub becomes progressively higher and squeakier until, by the end of the series, it's reached levels that pretty much only a dog can hear.
Waking Up Elsewhere: Sonic awakens after his fight with Dark Oak to find himself on a bed inside Dr Eggman's base. Turned out that the good doctor saved him from almost certain death and allowed him to recover his health during the week that he was comatose.
Wasn't That Fun?: Helen goes on a wild ride with Sonic in Episode 14 that takes them to and across an island in the middle of a lake where Helen says there is a beautiful patch of white flowers. The two are being chased by government troopers trying to catch them and bring them to the President's annual party honoring Sonic's heroics against Dr. Eggman, and with Sonic's speed and attitude and all that, he and Helen have never had this much fun together in a long time.
Yank the Dog's Chain: When Amy tries to use a spell to win Sonic over...and it just makes Tails and Cosmo fall in love instead.
Year Inside, Hour Outside: When Chris finally manages to get back to Sonic's world via Knuckles' Master Emerald during the Metarex Arc, he is suprised to learn since in their world, its only been a month since Sonic & Co. Went home. In Chris's world, six entire years have passed. There are side effects...
This is made even more confusing given the contradictory example in the first season finale, where Sonic finally arrives in his own world, where six months have already passed.
YouTube Poop: A popular source, particularly Knuckles saying "Shut up!"; also the theme tune Gotta Go Fast is played whenever a character is running. Probably inspired by the heavy use of Adventures of Sonic the Hedgehog in poops.