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.
Esteem. He sees absolutely nothing wrong with murdering his own wife when she discovered his plan to overthrow Celestia, subjecting Rarity to Training from Hell to teach her bladecasting, jamming a Artifact of Doom into Twilight's eyeball to turn her into Titan's puppet, ruthlessly slaughtering any of his superiors and subordinates who refuse to support the new regime, and all on behalf of the Eldritch Abomination he worships.
Cry for the Devil: Terra gets a flashback chapter that shows how she became the way she is: she had to Mercy Kill her brother/husband after Discord corrupted him, then Titan killed her mother for "betraying" him, forced her to be his new wife, and subjected her to the Insanity so that she'd become as brutal as him. It's kind of hard not to pity her after reading that.
Fridge Horror: Twilight gained the power of Queen Harmony, becoming able to match Titan, right? And then she drains Titan dry of magical power, effectively becoming twice as powerful as him. I don't remember it being mentioned anywhere that she gave any of that power to anybody else, either. Just think that Titan almost destroyed Equestria and was able to steamroll Princesses Celestia and Luna, both of them at once, with half the power Twilight Sparkle now possesses. Now imagine what would happen if Twilight Sparkle went rogue. There is literally nothing in Equestria, probably nothing in the universe that could contain her.
Fridge Logic: Apparently Nihilus used an Illusion spell against Rainbow Dash. But to what purpose, considering that during the early phases of the possession Nihilus looked just like Twilight Sparkle?
Harsher in Hindsight: Pinkie Pie knows every pony in Ponyville. Which means she knows everyone who died during Terra's attack on the town.
Hilarious in Hindsight: Months after Twilight became an alicorn in the penultimate chapter, the epilogue with her coronation was posted the same day that news broke about her becoming an alicorn princess in the season 3 finale.
Moral Event Horizon: Assuming he hadn't crossed it before, Titan using the Insanity on Terra to force her to kill thousands of ponies certainly counts.
Never Live It Down: Apparently one of Harmony's earliest creature designs involved flaming hyenas. Though the "flaming" part may well refer to the way the alicorns exterminated them.
They Wasted a Perfectly Good Plot: Pinkie's nature as an arcpony can be seen as this. While Fluttershy uses her similar status as an eraterus to pit the most powerful dragon in Equestria against Titan, in Pinkie's case it does not really serve any purpose except explaining her powers.