Ass Pull: While this series is no stranger to breaking the fourth wall, for the most part, it's only ever done for a gag, especially in the early seasons. However, there are two cases where this is used to move the plot along.
In the Niagara Falls episode, Scott and Dawn are able to win the tightrope challenge despite having other players in front of them by "godplaying." While this likely doesn't effect the boot for the episode, there was no precedence for Dawn to break the laws of physics alongside another human, and the idea is never used again.
In the final eight from Pahkitew, the Author Avatar emerges, breaking the fourth wall to create drama. While this event is reset after the fact, Fallon remembers the events, due to her natural power, and this contributes to her decision to leave the game.
The Beauty Queens in Ridonculous, as to whether their overprotective behavior towards Ezekiel against Giselle is justified of not by their having faced homophobia at her company.
Giselle herself — some think she's a genuinely sympathetic and cute character, while others see her shtick as annoying and think she deserves to be talked down by the Beauty Queens.
Big-Lipped Alligator Moment: The very end of the second Celebrity Manhunt when Felicity turns into Applejack and returns to Equestria.
The April Fools episode is just the word "Mayonnaise" repeated over and over, a Shout-Out to Rocko's Modern Life.
"Error! Sanity Not Found" has the author enter the fanfic and use Author Powers to exploit the contestants' trauma, even showing them scenes from canon. Then their memories are wiped and the whole ordeal is never mentioned again. Oddly, the episode does have some serious plot relevance afterwards due to the reveal of Colton and Abigail's supposed relation.
Creepy Cute: Baby Fang. He's the same scary land shark as canon Fang... but now much smaller and bright-eyed!
Growing the Beard: World Tour was when the series took on a more responsible tone, included more diversity, cut down on inside jokes and meme references. All Stars solidified this while also beginning the Darker and Edgier tone of the series.
Cogreen: I WAS WRONG. I WAS SO WRONG!!! OH MY GGOOOOSSSSHHH
Then with the reveal of Devin in Ridonculous Race, three years after the fanfic began:
Cogreen: *looks at the guy* ... *looks at his appearance* ... Oh yeah.... *notices how the name ends in an "IN" ... Oh my... *looks at his description* ....Athletic... seems unaware of the crush directed at him... and is likely to become intertwined in a romantic relationship with a blonde girl voiced by Kristen Fairlie...Guys, I can't believe Shin is participating in Total Drama: Ridonculous Race. I'm honored.
Coby, who entered the series in Revenge Do Over, strongly resembles Junior, who was added in canon Ridonculous Race a few years later.
The reasoning for CoGreen eliminating Leonard first is, "I eliminated him first since we're going to be seeing more of him in TOTAL DRAMA Ridonculous Race." Said character was eliminated first in Ridonculous Race as well.
Noah's phobia in TDIDO's Phobia factor is lawyers, when in canon, he winds up dating Emma, a lawyer in training. This is acknowledged in "Error! Sanity Not Found."
In "Can't Help Falling In Louvre", Lightning sees up Lindsay's skirt when she runs through the lasers. Mel commends him on this.
Melzy tends to get a lot of subtext-y scenes, but the bobsledding scene in "Jamaica Me Sweat just pushes it to the extremes. It's even lampshaded in an annotation. Both Mel's owner and the fic author consider it canon in a Friends with Benefits sense before Mel realized she was bisexual.
Charlel in the Halloween special. Later in "Post Plunker's Paradise", Mel calls up Charlotte, calling her the "only one who understands" and being welcomed to her house anytime. The belated recognition of the subtext is why they became an Official Couple in Pahkitew.
Mel/Courtney have shades of this, notably in "Chinese Fake Out" when Mel assumes Courtney wants a "goodbye gift" before presumably being voted out. In Pahkitew, it's also retroactively implied that Mel was attracted to Courtney as she realizes she's a Serial Homewrecker because seeing her boyfriends' ex-girlfriends get angry at her turns her on.
Despite a history of manipulation and brute force against her competitors, seeing Mel berated for her sexuality and hating her behavior in Pahkitew is pretty harsh.
Mal. Despite committing some heinous acts in canon, including serious injury, domestic abuse, sexual harassment, and attempted murder, he reveals in "Defiled" that he's a victim of some serious Parental Abuse and has spent his whole life being shamed for existing.
Colton, despite all his frigid behavior, due to his Freudian Excuse. His father was disbarred on assault charges and he lost his sister in Afghanistan, which is why he acts so distant to everybody else.
Scarlett, even moreso than in canon. Whereas in canon she only has one episode as evil, here she nearly kills the other contestants on a regular basis, eliminates almost everyone, and plans to sell the radioactive creatures in a terrifying bid to take over the world.
Mal, even moreso than in canon. The kiddy aspect of Mal's malevolence is gone, and with it comes brutal instances of his violence. From abusing Zoey and causing her to break up with Mike, to forcibly ripping out Duncan's tooth. There's also the twist in Defiled where Mal is revealed as the original personality, and created Mike as an escape from an abusive childhood.
The Wawanakwa Blue Moon is very unsettling, as it not only affects the animals, but changes the humans. For starters, Mal is released, both Brick and Bridgette become ax crazy, and the normally silent B uncharacteristically yells at Sierra and causes her to flee in fear.
Rescued from the Scrappy Heap: Robert in All Stars, originally one of the most hated original characters by fans and writer alike, became more popular due to his Heel–Face Turn after becoming friends with Leshawna.
Tear Jerker: Courtney becomes incredibly despondent after Duncan breaks up with her. Seeing her so broken down is horrible.
Courtney: I just wanted to be alone… seems to be what everyone wants me to do anyway…
Noah has a breakdown after Dakota tricked him into thinking that Abigail broke up with him via forging a letter. "Oh My Abby" is considerably sadder than "Oh My Izzy."
Zoey's elimination in Saving Private Leechball, before which she is blamed for lying about Mal's abuse.
The reveal in "Defiled" that Mal is the real personality and that Mike was created because of parental abuse, including distressing flashbacks to his childhood and the reveal that Mike was created so Mal would appear to be a good child.
Colton and Abigail fighting over possibly being related. Colton has already lost his sister and is completely shaken at the idea of having another one, while Abigail hates that Colton's pushing her away and making her feel inferior, and struggles with the idea that she might be a Child by Rape.
Vanessa in Action, after starting to turn a new leaf, suddenly snaps back into meanness. As it turns out she was kidnapped and impersonated by Heather for about a quarter of the season.
Nathaniel in World Tour gets pinned for being evil based solely on a few bad coincidences and coming off too nice to be genuine.
Charlotte, after losing her memory, which is bad enough in itself has to deal with Trent becoming possessive, going off the rails in the process. This has ripple effects on Mel, who struggles to find acceptance, and Ella, who had a tough childhood.
Abigail is generally quite perky, which makes it sting more when certain seasons put her through the wringer. In Island, she's the target of Heather's constant bullying and attempted public humiliation. In Pahkitew, she's constantly made to feel inferior, especially in "Error! Sanity Not Found" when she learns about Noah's canon girlfriend Emma and has an existential crisis. Then comes the reveal that Abigail and Colton in Pahkitew are ambiguously siblings, wherein Abigail may have been conceived by rape. This was thrust upon both of them mid-season, making an already tough situation even harder to process.
He's the same scary land shark as canon Fang... but now much smaller and bright-eyed!