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.
And whatever the music is that plays towards the end of episode 8, where Niiya finally gets himself together and heads back to the clubroom and Yuuko.
Requiem plays in episode 12 when Yuuko fades away.
Esoteric Happy Ending: The manga ends with the HEAVY implication that Yuuko dragged Teiichi to the other side. Yay?
The epilogue repairs this by showing that Teiichi is still alive and that Yuko is still around to be with Keichi. It also ends with heavy implication that they'll spend the rest of their after/lives together without Keichi dying.
Family-Unfriendly Aesop: Quite a few times the Paranormal Investigation Team decides to used Yuuko's ghostly presence as an excuse for another characters actions rather than have the character accept what they've done (they usually still learn their lesson, but receive no punishment for dangerous and/or illegal acts). Most of the time their actions end with "Oh look! It really was a ghost and I'm completely innocent!"
Momoe and Kirie in chapter 19, and Kirie towards Yuuko in chapter 20.
The entire Six Year Sakura story.
Moral Event Horizon: Yukariko breaking Yuuko's leg and entrapping her in a basement for her to die.
The bullies attempting to sacrifice Yuuko (the living one, not the ghost one).
Narm: When Kirishima is about to be sacrificed, her captors choose to tear open her shirt and invoke some Gainaxing rather than actually hurt her. For this troper, the drama and suspense was immediately diffused.
The author confesses to not being interested in adult women in the commentary on the swimsuits in the chapter 13 omake.
Actually, with the way original Japanese sentence is worded, it could be interpret as "This corner doesn't call for the adult" instead of the Scanlator version of "I have no need for an adult". Which makes more sense since the manga is serializing on a Shounen magazine.
The revelation late into the series that Teiichi is only 12 years old.