Designated Hero: Mary's harshness towards Colin is presented as right, because he changes afterwards, but most, if not all of what she says, is as applicable to her, as it is to him. Also, in the film version, when Mrs Medlock blames Martha for letting her in, Mary doesn't say the truth, that Martha had nothing to do with it, and actually tried to stop her. It is Colin who orders Medlock out. To be fair, even Medlock's not complete Jerkass as she clearly does care about him and her duty.
It Was His Sled: On the first time through the book, Colin's existence is quite a shock.
Jerkass Woobie: Colin and Mary both, pre-Character Development. They're spoiled brats and rude to everyone around them. But that's only because they've never been shown love from their parents and have grown up essentially alone. Through others being kind to them, they are able to become nicer people.
Nightmare Fuel: The mere fact that Mary spent who knows how long wandering around an estate full of dead people, not realizing what's even going on. If the soldiers hadn't showed up, she might well have starved, surrounded by decaying corpses.
Toy Ship: A three-way version. Mary has Ship Tease with both Dickon and Colin. She's not paired with either, allowing shippers to fill in the blanks for themselves.
In 1911, The British Empire was in full swing, and it shows in this book. Indian people are referred to as "blacks" and they're considered less respectable than white people. The narration even refers to Mary having used violence against her servants in the past.
On a less serious note, Mary, a ten-year-old girl, is often and bluntly referred to as "ugly" by both the narrator and other characters and often to her face. Also, compare the approving references to her getting "fatter" (i.e. healthier and less scrawny) with today's concerns with obesity.
Mrs. Medlock, and even some of the more sympathetic characters like Martha and Mrs. Sowerby, also often refer to Mary as sour, contrary, or with adjectives that indicate a perpetually bad attitude. One wonders how much self-fulfilling prophecy played into her character.
Also, this: "She used the wrong Magic until she made him beat her." Ben Weatherstaff mentions a woman in the local village who nagged her husband until he beat her up and left for the pub. Colin's response is that she used the "wrong Magic" and Ben agrees.
More a case of Society Marches On, but we're supposed to see Mary - at least through Martha's eyes - as dysfunctional and hopelessly coddled because at the advanced age of nine she never goes anywhere by herself. In the same part of the world now, Mary would be at about the minimum age that children would start going out of sight of home without an adult.
Mary's treatment of her Indian servants - including getting violent towards them - is used to illustrate her as a Spoiled Brat. Martha also scolds Mary for her racist attitudes when she gets angry that Martha thought she would be an Indian. That's not to mention that it's implied that bringing a little girl up to believe that she's inherently superior to those around her - even her caretakers - is what made Mary so dysfunctional in the first place.
The book is also surprisingly ahead of its time for criticising neglectful parenting among upper class families. Both Mary and Colin are spoiled and dysfunctional because they've essentially never been raised by a proper parent. Mary's parents ignored her and had her servants take care of her - and as a result she grew up into a cold little brat, with huge abandonment issues. The story shows that even non-malicious neglect can still cause problems. Lord Craven is just too afraid to care for Colin in case he dies like his mother - but the lack of attention he showed his son still had a negative effect on him. The story points out that children do need love and proper care from their families - in an era where upper class children would still be sent to nannies and governesses, and treated more as heirs to pass property onto.
Wangst: Colin is like this until Mary gives him a good talking-to.
The 1987 version uses Chopin's Nocturne in E Minor, Op. 72, #1 as its theme music.
The 1993 film has some very beautiful theme music, too.
The score for the 1975 miniseries? Yeah—freaking awesome.
"Lily's Eyes" and the various Storms in the musical version.
Big-Lipped Alligator Moment: The 1993 film has a scene where Colin is taking photos of Mary and Dickon on the garden swing. When they look into each other's eyes rather lovingly - for too long - Colin angrily says "hey!" and looks furiously jealous. A love triangle between Mary, Dickon and Colin is never explored, Mary doesn't show romantic interest in either boy again and the incident isn't mentioned again. The very next scene has the children playing happily together only a few minutes later.
The 1993 film and the anime series designate Mrs. Medlock as an overbearing caretaker, even though in the book her initial antagonism fades as the narrative progresses. Although, even in the 1993 movie, she genuinely believes her treatment of Colin is what he needs to make him better, while Mary probably does need to learn to be more self-sufficient and less spoilt. Also, she, like everyone else, is moved to tears at the climax.
The musical designates Neville Craven, a doctor whom Mary accuses of wanting Colin to die so he can inherit his brother's estate while it's never stated whether this is true or not, he's still the primary antagonist. In the book, he is in fact a deeply caring man who took up medicine to help his older brother.
The anime series not only does this to Medlock, but creates a character for this: Max Hawkins. He actually turns out to be a decent person once we get to know him, but he was badly broken in the past and thus he can't forgive Archibald Craven for his Break the Cutie experiences.
The 1987 film has a bit of this outside of the story. Since the film makers made it so Colin and Mary aren't related, they had to get rid of Dickon. The only way to do that was to kill him.
The sequel to the 1987 version Back to The Secret Garden also does this when Dickon gets a fair bit of mention from Martha and Mary as he died in the war before the end of the last film resulting in Mary and Colin ending up married.
Speaking of Back to The Secret Garden, Lizzie Buscana is a Heartwarming Orphan who travels to Mistelthwaite Manor from America at Lady Mary Craven's request to take the place of one of the orphan's now living at the manor in desperate need of surgery at an American hospital. When Lizzie arrives she quickly gains two Love Interests in the form of Robert and Steven, orphans who now live and go to school at Misselthwaite Manor.
Lizzie and Robert become an Official Couple during their Fetch Quest to find the original door to the Secret Garden which was replaced when Martha Sowerby was unable to find it after Mary left for America with Colin.
In any of the film adaptations, Mary walking through the house to find Colin can be deeply unsettling. The 1987 version takes this Up to Eleven with scary music and a lightning storm raging outside the manor — and let's not forget the cutaways to the light playing off of the dark, ugly statues.
There's also the opening from that same movie, where Mary's wandering through a house where everyone except her is dead or dying from cholera, and she doesn't even understand what's happening. Special mention goes to the lingering shot on Mary's dying parents, with their faces twisted up in pain.
The 1993 film replaces the cholera epidemic with an earthquake. The scene built around said earthquake, while short, could still be a case of Nightmare Fuel.
The 1993 film also gives Medlock a very creepy Leitmotif.
The Dreamers in the musical, especially in the various Storm songs.
Rewatch Bonus: The 1993 film has a sequence where Mary in her first morning wanders around Mistelthwaite and finds her aunt's room. She hears crying and Medlock shouting "Martha!" - which turns out to be Foreshadowing that Colin is hidden away in the house.
The anime series gives us the Canon Foreigner Camilla. She and her mother were hated for being Roma, then her mother dies, later Lillias takes Camilla in as her lady-in-waiting and she falls for her young accountant Hawkins... and loses them both, so she has to leave the Craven's manor while being accused of killing Lillias since she got up the tree to get her a gorgeous flower as a birthday gift. She is epically broken, and it's a miracle she doesn't commit suicide or something and remains kind to Mary.