Crazy Awesome: Pinkie Pie. What else do you call a pony who tricks a squad of Royal Guard programs into behaving like a random encounter in a JRPG? And invent a thought controlled omni-tool, something every other species has failed to do, on a coffee binge? Deconstructed in that her methods wasted lots of resources and put her wellbeing at risk, which Twilight warns her they can no longer afford.
Fridge Brilliance: Equestria's Sugar Bowl nature makes perfect sense when you consider that is a combination of both Celestia's over protectiveness of her charges, and a hold over of its original purpose as a combination luxury resort/propaganda showpiece for Epona Systems to allow various sentient species to experience an ideal Equine society.
It also explains a lot of the Fridge Logic of the show, like the Royal Guards being so visually alike (they're defensive programs), any examples of Chaos Architecture, the monsters and foes the Mane Six have faced turn out to be challenges by Discord or disguised errors in the system, any OOC moments (the systems messing with their heads), and the animation errors and multiple instances of background ponies in the same scene (errors in the simulation and changeling programs filling out the scene, respectively).
Informed Wrongness: Applejack's questioning of Twilight apointing her Head of the Equestrian Board of Directors and Acting Vice President, despite her recent scandal, is shut down when Twilight insists that it proves she can be counted on to whatever it take for the good of the Herd. This overlooks that the scandal was done not out of conviction, but ignorance of the severity of the legal consequences, with Applejack second-guessing her actions upon realizing this. Compare Rarity, who's political play has caused nothing but good, while Applejack's qualifications are only mentioned in the Codex, but never shown in-story. Add it happening minutes after Rainbow Dash was gravely injured and such a big decision is normally left up to readers, it supports Applejack's concern as Twilight seems to be acting when emotionally compromised, which 42 of 50 had previously warned her about.
Moral Event Horizon: Milligan crosses it when he tries to convince Shepard to download the Equestrian servers, which would have killed all the ponies, despite knowing that they're sentient beings, condemning a species older that human sentience to extinction. Played with in that how much of this is due to Discord's brainwashing him (thus discord's MEH) as opposed to his choice is ambiguous.
Stoic Woobie: 42 of 50 is the Sole Survivor of the Equis civilization, with the last memories of all that was lost, which would be tough enough. He's now a vital Living Emotional Crutch to Twilight, the one pony keeping what remains of them going, blames himself for every minor mistake, and know his being an AI would damn them if discovered. He cannot afford to show much emotions, and envies non-sapiant changeling drones for being genuinely emotionless.
What An Idiot: Applejack at the start of the second arc of Shades of Twilight. After being given reason to suspect that Dr. Hern is in danger, you'd expect she would inform the authorities or anyone else. Instead, she abducts Dr. Hern from the hospital and tries to hide her away, which predictably blow up in her face.
The Woobie: The Equestrians are a Woobie Species, living the happy life from the show, then suddenly forced out of their world, finding that it, their material worth, and many of their friends and family were nothing more then simulations that are now lost forever. Their now trying to make it in a galaxy that would discriminate against and seek to exploit them, with little more then each other and some basic galactic knowledge going for them. There's still some stand out individual examples.