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.
Harsher in Hindsight : At the beginning of the week, Miki is finishing cleaning up a hallway. Taichi briefly wonders if maybe she's running away like Misato is through cleaning. And then her own week comes around and she reveals the hallway was covered in bloodstains of someone that is most likely Sakakibara, one of their teachers. Since blood makes him go berserk, that's bad enough. The only thing is, she was probably killed by an alternate version of Taichi himself going berserk.
Tower of Friends reveals that it was that world's Miki.
Taichi's earlier comment about how Touko would be moved enough by Titanic to jump into the ocean with her boyfriend sounds much worse when you realize he isn't kidding.
Also in Touko's route, Taichi tries to dissuade Touko from pursuing him, saying how his family has a record of extremely short lives. His father died before he was born. His mother died not long after.
Taichi and Yutaka's exchange lines about how it feels like they've met before and how Taichi may have a score to settle with Yutaka. That's because Yutaka essentially helped make Taichi's life a living hell during his childhood.
Nightmare Fuel : Tower of Friends. It does not mean a tower built with friends or anything. No, it's how the alternate world's Taichi suddenly went insane one day, killed that world's version of the game's cast and built their corpses into a broadcast tower.
Squick : Taichi's behavior during the latter parts of Kiri's route is rather... unpleasant. It's the route that really introduces just how messed up Taichi is, so the writers pulled no punches in making the point. During the final route, you get to see a different version where Taichi uses the knowledge from the notebooks to avoid all the really disgusting scenes.
Tear Jerker: "CROSS X CHANNEL", the final route. Counts as an in-universe example too, seeing how Taichi started crying, something which he thought wasn't possible.