Due to their similar hair colours and shared background as farmboys, it's a reasonably popular idea that Rodney is in some way related to Scott (either as a cousin or a brother, since Rodney states he has many brothers). A few people headcanon Crimson and Scott to be related too, since de-gothed Crimson has a similar hair color and eye color and spent her childhood on her grandma's farm. Some fics even make her real name "Albertha," the name of Scott's sister whom he mentions in All Stars.
Fanworks love to bring up the idea that Dave and Noah are related in some way (usually as cousins) due to their similar designs and personalities.
Given that Dakotazoid is an obvious Shout-Out to The Incredible Hulk, fanworks that feature Dakota being reverted to her human self usually add to the allusion by giving her the ability to turn back into Dakotazoid through anger. Ezekiel is also sometimes given a similar ability regarding his feral state, albeit on a lesser scale.
Fanworks often give Mike a more realistic DID system, giving his personalities reasons to exist and protect Mike just like real alters do.
Mal is a persecutor and/or protector who acts out either from self-hate, resentment towards Mike, or to protect the system.
Svetlana is a protector formed from physical assualts.
Vito is assumed to be a holder of sexual trauma, since he's a huge flirt triggered by Mike's shirt coming off.
Chester is usually an introject of Mike's grandfather, or other elderly figure in his life.
Manitoba Smith is a fictional introject based off an equivalent to the Indiana Jones movies.
People like to imagine Ella and Dawn, both colorful, All-Loving Heroine characters from separate casts, becoming fast friends or romantic partners.
Due to their similar physical appearances and narcissistic personalities, some fans toy with the notion that Topher is Don's son.
To explain Courtney's uptight, perfectionist personality and lack of social skills, many fanfic writers give her a Freudian Excuse in the form of demanding, unpleasable parents who expected her to be completely perfect at everything, never allowed her to do anything but focus on academics, and/or would react badly whenever she didn't get 100% at something growing up.
Molly, Zoey's prototype design from Total Drama Reloaded, is often made an Ascended Extra who is included in various ROTI fics to round out the cast to 14 competitors.
Lightning is often thought to be attracted to men, due to a combination of how he reacts (averting his eyes and biting his lip) when Sam says to Scott "You kissed a gentleman?" and the "Lightning don't judge" scene in "A Mine Is A Terrible Thing to Waste" when Jo, whom he believed was a boy, tells him that she has never kissed a guy before, which establishes that he is, at the very least, supportive of gay people.
Since the three most popular Jo ships (Jo/Brick, Jo/Anne Maria, and Jo/Lightning) are all with people who she often bickers with, many fans like to interpret Jo as a particularly harsh Tsundere.
Even though Scott's fear of sharks only appears after he was mauled by Fang, many fans write him with a phobia of sharks from the get-go, particularly in alternate universe fics where he competes in the "Phobia Factor" challenge.
Since there's so little backstory to her, Ella being so over-the-top cheery is often headcanoned as a coping mechanism for an impoverished home life, with her interest in fairy tales getting her through tough times as a child. There's only a smidge of canon support for this as she lives in an apartment with thin walls.
If Sierra gets an Freudian Excuse, it's that: she had a very dysfunctional childhood. Her father is either dead or simply not in the picture (it varies whether he left them or divorced Sierra's mother). It's often believed her mother became a Stalker with a Crush for Chris afterwards. Due to the fact it's heavily implied she is also a Loony Fan and encourages her daughter's own stalker tendencies, her mother is often depicted as more crazy than her daughter or at least unintentionally neglectful. Thus Sierra developed a tendency to cling on to things to an unhealthy level which brought her to her stalker tendencies.
Courtney typically earns an Odd Friendship. In the older days, this was filled by Izzy. Nowadays, it's more likely to be filled by Lindsay.
Blaineley is typically either the mother or aunt of Amy and Sammy. With the series' reboot happening, there's also been a recent influx of people who theorize she's related to Julia.
Due to how similar they are, many have thought Harold and Scarlett as siblings. Izzy is sometimes also included.
Several fans like to think that Scarlett was genuinely a polite and shy nerd rather than an act but underwent Sanity Slippage thanks to Max constantly frustrating her.
In fanworks where Sierra is in a cast that doesn't have Cody in it, Sierra is either in love with someone else, fawning over Chris for her mom, or simply enjoying being on TV. Depending on how the author views her, she'll become a nuisance like she did in canon or she'll have character development and start to lose her stalker tendencies.
Thanks to their pale skin tones, similarly colored eyes, and creepy mannerisms that freak out everyone they come across, theories about Scary Girl and Dawn being related (or, in the most extreme cases, Dawn being Scary Girl in disguise) have begun to pop up in the fandom ever since Scary Girl's design was shown.
Even though this show and Total DramaRama are confirmed to be completely different universes, many fans have latched onto the idea that Gwen and Ella and Owen and Max are cousins in the main series as well, with fanfics portraying their relationships accordingly.
If an author is trying to give Duncan a Freudian Excuse, it's generally that his dad, who was shown in his video from home to be ashamed of him and even directly questions if he and his wife love him, was abusive towards him and Duncan became a criminal both to act out and to spite his cop father. On the flip side, his relationship with his mother is usually more positive, due to hints that Duncan is a bit of a Momma's Boy in canon.
In fanart, it is very common for MK to be depicted as having pride pins on her beanie and jacket.
Amy and Scarlett are sometimes imagined to have a Villainous Friendship with each other. Max can be included too.
(averting his eyes and biting his lip) when Sam says to Scott "You kissed a gentleman?" and the "Lightning don't judge" scene in "A Mine Is A Terrible Thing to Waste" when Jo, whom he believed was a boy, tells him that she has never kissed a guy before, which establishes that he is, at the very least, supportive of gay people.