These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
The TV Series
Genius Bonus - The morse code at the beginning of every episode spells something out, which also counts as something of a Couch Gag.
Growing the Beard - The second half of season one, in many viewer's opinions, once the characters stopped behaving like idiots, the drama became dramatic, and Emily got significantly less screentime.
The Woobie: Cards. Poor Cards. Her life is shit. To wit:
Cards is a loser and partial outcast in her own community. She's also small, weak, pathetic, unloved, emotionally unstable at times, and is unable to ever catch a break. Plus, her mother is abusive towards her. Add to that the fact Cards is also sexually unsure of which gender she likes and the fact that it doesn't matter because she's so much of a loser that she could never hope to get laid even though she really would like to.
In her first appearance, Cards hatches a plan to earn her town's respect, which, due to a case of Mistaken Identity, ends with Jericho murdering her best and only friend, and then Jericho essentially bullies and intimidates her into helping him out on his quest.
She emotionally destroys herself when she accidentally kills Brave Boulder, an agent of the Government Conspiracy, since she never meant to kill anypony. And when she cries about this to Jericho, Jericho openly smacks and berates her for feeling so depressed about what he viewed as a heroic deed.
After Jericho again verbally demeans her as a person, Cards goes off with a buck named "Social Grace", who appears to want to help her against Jericho. This results in them going on a nice date, only to end as Social Grace reveals he was actually working for Duke Elkington; that the earring he gave her was actually liquify her organs, and if she takes the earring off, it will kill her instantly; and that if she didn't obey and help him, he'd kill her. It was also suggested but never said explicitly that Social Grace had tried to rape Cards during that. Only after that does Jericho show up, but "saves the day" by sawing off part of Cards ear to remove the earring without any painkillers, healing potions, or anesthetics only to shove the part of the ear down Social Grace's throat in order to liquify him.
When she returns home at the end of Act I, she is forced to bludgeon her own mother to death.
If Jericho's deduction is true, then sometime after Act I, Cards ends up as the Tin Mare of Hoofington, and very likely is suffering from post-traumatic stress disorder.
Jericho's narration constantly, constantly makes fun of Cards.
Ensemble Darkpony: Cards, by the way, is also this. Word of God says she was only meant to die in her first appearance, but got tacked on as a main character who was meant to simply die later. Several chapters and critical emotional and physical abuses later (see The Woobie above, especially including that dark scene wherein she's forced to bludgeon her own mother to death) and Cards is now the adorable fan-favorite, emotionally destroyed character everyone wants back, since the author made a choice not to include her in the story's second act.
Complete Monster: Jericho himself, by many accounts. If you strip away his bubbly demeanor and constant humor, he is sort of a mass-murdering sociopath with absolutely no care, pity, or empathy and is an adroit liar with absolutely no guilt or remorse for all but one of the actions he performs in the course of the story. In fact, it's been suggested that Jericho is perfectly aware of this, which is exactly why he's constantly trying to hold onto his bubbly demeanor and constant humor, all in an attempt to hide this essential fact. He even says that his Code Of Honor was created purely to prevent Jericho's more monstrous side from coming out.