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.
Fanon: The game quickly worked its way up after it was released, whether it be as a mention or an in-joke in another fanfic/fanwork.
It's actually Canon in the Pony POV Series. In the second season, the town's inhabitants have been recruited by Princess Gaia, having their memories erased. When they deal with Princess Gaia, the curse is still in effect, with them screaming how they didn't mean to forget, how they thought it was the plague their ancestors warned them about (see below).
Fanon Retcon: Story of the Blanks was released a few months before "The Cutie Pox" aired. Once that episode aired, however, fans incorporated the canon story into the fan-game's universe. The disease is a pretty good explanation for why the ponies of Sunny Town act the way they do about Cutie Marks.
Harsher in Hindsight: The ponies in Sunny Town killed one of their own fillies because she got her Cutie Mark.note The game never states outright or implies that Ruby was ever a native resident of Sunny Town. In fact, it is just as likely that she wandered in just like Apple Bloom did, and just happened to get her cutie mark while there. "The Cutie Pox" gave us the eponymous disease that causes ponies to get multiple Cutie Marks, forced to perform whatever talent the marks represent against their will, and make others run in terror of being infected. Now replay the game with these in mind.
Not to mention the fact that one of the ponies in "The Cutie Pox" said something similar to a line from the game...
Lily: (about Applebloom) She's cursed!
Three Leaf: (about Ruby) The curse had befallen her this very night. She had the Mark! She had to go!
Another thing to consider: Who is the character you play as in Story of the Blanks? Apple Bloom, who happens to be the starring pony in "The Cutie Pox".
Applebloom wanders all by herself into a scary, dark forest in season 4 episode "Somepony to Watch Over Me". She doesn't encounter zombies and is instead confronted by a chimera, however.
Hell Is That Noise: The looping sound effect that plays when Apple Bloom discovers Ruby's charred corpse in the fireplace and when the Bone Fiends find Apple Bloom and Ruby.
Barring some aesthetic qualities, the Changelings resemble the Nightmares in several manners.
It's Short, so It Sucks : The biggest complaint about this game; even favorable comments frequently comment on its (lack of) length. If you know what you're doing and don't dawdle, you can beat it in about ten minutes.
It Was His Sled: Most fanworks based on this don't even try to hide that Sunny Town is composed of Nightmares, that Pony you've been chasing is named Ruby and she's dead, or that Apple Bloom becomes one of Nightmares if you fail to escape.
Nightmare Fuel: Just thinking about this game after playing it can make the effect it had worse.
That One Boss: Starlet. Admittedly she'd be less infuriating if the player didn't have to watch the haunted town cutscenes and walk all the way back to her just to try again.
The Woobie: Ruby, who is forced to spend eternity with the ones who murdered her. Mitta qualifies, having had the choice to protect Ruby but chose not to, and is thus forced to serve in the punishment as well.
In the Pony POV Series it gets revealed at one point that Ruby could have left after death, but she stayed behind when everypony else got cursed (by Nightmare Moon, no less!) because she pitied the other ponies and refused to leave until they were all redeemed.
Let's not forget poor Apple Bloom herself. Poor girl had to endure some serious horrors, despite being but a wee filly.
Heck, the townsponies could qualify as well, depending on how you view them. Nopony has their cutie mark, normally viewed as a natural and expected occurrence in ponies. The entire town has grown to see marks as a bad thing, so almost no one has discovered their "special talent" for fear of being killed.