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.
Fridge Horror: Obsidian never was reincarnated in the story, meaning the Order Triune had been trying to kill an innocent man for nothing. The Order Triune has supposedly wiped out Obsidian before, but since he never resurrected, how many innocent ponies could the Order have killed before?
At least one event that is infamous for leading to many many ponies dying is definitely due to The Order trying to kill a pony they thought was Obsidian. It couldn't have been him, as he was sealed about 1200 years ago, but there is mention while talking about his returns early on of one event 700 years ago. And the Order's attempt to kill that particular "Obsidian" lead to the pony version of the Titanic disaster.
The Gatekeeper's line in chapter 24 implies that this might not have been the first time Obsidian attacked Earth. The only reason Obsidian never reappeared on Equestria was that he was too busy trying to invade Earth.
"Funny Aneurysm" Moment: You know, come season 3, Twilight's the one who, in-canon, if she and the other ponies were human, has broken the Laws of Magic (specifically the prohibitions against mind control, as per Lesson Zero, time travel, as per It's About Time, transforming others, as per The Cutie Mark Chronicles, and arguably, killing people, as per Too Many Pinkie Pies). At least by Magic Duel, Trixie's now a repeated Second Law breaker.
The passage in Chapter 10 of False Masks where Harry talks about what it looks like when a father loses his child is kind of hard to read in light of Changes.
Episode 5 of season 3 Magic Duel features the Great and Powerful Trixie using a dark source of power, that corrupts her to get revenge on Twilight Sparkle. Pretty much the concept of Strange Friends sans Dresden.
False Masks has its own funny aneurysm moments: that comment Michael makes at the beginning of the story about being called to drive Harry to wherever? That's probably where he first saw Obsidian. Bob noting how empty the Nevernever is on the Way to Equestria? The corpse dragon that ultimately kills Novel Notion is likely responsible... AND IT'S HUGE.
Hilarious in Hindsight: The one off 'Extra stuff' of Maggie writing her own fan-fic where Harry marries Twilight and then takes her to live in Equestria with them got a whole lot more plausible come Skin Game when it's revealed Maggie really is a fan of the show.
Novel Notion's extermination of the entire Order Triune to summon a demon. The fact that they all were demented zealots who more or less brought it upon themselves does not weaken the horror of the act.
Nightmare Fuel: Harry being possessed by the Nightmare in Strange Friends.
We finally learn why the Order Triune is so deadset on destroying anything even remotely resembling Obsidian in False Masks chapter 14. Obsidian's corpse after his first death disintegrated anypony who touched it as well as anyone who came in contact with the black vapor surrounding it. He then resurrected himself 50 years later and tried to take over Equestria AGAIN.
Novel Notion/Bookmark sacrificing nearly the entire Order Triune to summon a Demon. Even the heroes are horrified.
The real Obsidian being powerful enough to give two Knights of the Cross, a veteran Warden, and the Gatekeeper a run for their money before apparently being permanently slain by Michael gives Harry the chills.
One-Scene Wonder: Doctor Whooves' second cameo in chapter 20 of False Masks, where he gives Harry a pep talk and reminds him just how hard the mane six would take his death if he ran off after Novel Notion on his own.