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.
Epileptic Trees: By its very nature, it's designed to make you question just what is going on.
Genius Bonus: The images on the walls and bluffs. Some of the chemical formulae are ethyl alcohol and dopamine and at least one of the electical diagrams is for anti-lock brakes. The writing on the walls is a reference to the biblical story of Paul's journey to (and conversion at) Damascus.
There's also a golden spiral on the beach. It's more or less unexplained.
Faux Symbolism: Lengthy Biblical references, Arc Numbers, drawings of molecular structures on the walls of the caves. What do any of these mean? Good question.
Nightmare Fuel: In an intellectual way - not so much visceral. Aside from the narrator describing in vivid detail his broken, gangrenous leg, of course.
The detailed and entirely first person cutscene of the narrator climbing the island's radio mast then throwing himself from it. Though just before he hits the floor, it turns into a sort of Heartwarming Moment.
Tear Jerker: Despite the narrator's weird, poetic way of speaking and possible unreliability, you'll probably end up feeling sympathy for either him or one of the characters he mentions.
“I collected all the letters I’d ever meant to send to you, if I’d have ever made it to the mainland but had instead collected at the bottom of my rucksack, and I spread them out along the lost beach. Then I took each and every one and I folded them into boats. I folded you into the creases and then, as the sun was setting, I set the fleet to sail. Shattered into twenty-one pieces, I consigned you to the Atlantic, and I sat here until I’d watched all of you sink.”