After the revelation in the manga that Kafuka was Dead All Along, a lot of the nonsensical symbolism in the show (particularly the opening and ending sequences) now suddenly makes sense as Foreshadowing when you realize that a lot of it can be interpreted as metaphors for Kafuka's true nature, as well as her ability to possess her classmates. It also explains how she is seemingly everywhere all the time.
Zan's opening has a short sequence where all the girls are singing but only Kafuka's voice can be heard.
Episode 3 of Goku's opening has all the girl turning into Kafuka one by one. In manga, there's also a similar occurance. In "Seeing the True Color" chapter, Abiru's eyepatch falls off, she sees that almost everyone in classroom are Kafuka, including herself when she sees her reflection on a mirror. This is also the first time any of the girls realizes about the phenomenon.
Zoku's opening shows various body parts, hinting on how Kafuka donated her organs after her death.
The original anime's opening has a lyric that says "アタシがいるよ気付いて… (you just need to realize that i'm here)". A subtle foreshadowing on how Kafuka's spirit possessing her classmates since the beginning.
There's a LOT of foreshadowing in the anime (which made people wonder if Shaft was in on the whole thing), for example:
In Episode 4 of the first season, Kafuka (while posessing Abiru) wants Meru to look into her left eye. Kafuka's left eye was actually transplanted to Abiru. She also has Abiru's bandage on her right hand.
Kafuka briefly voiced Meru in Zoku Episode 13. Meru actually got her voice from Kafuka. Not to mention that Meru was teased to the point of refusing to speak because her voice sounds funny, presumably from the operation.
Chiri makes a realistic-looking heart-shaped chocolate for Nozomu for Valentine. The organ which she got from Kafuka was her heart.
In the Hot Springs Episode, Kafuka is mysteriously absent after the girls are detoxed. This probably means they have been purified from Kafuka's influence. Kafuka returns right after they get toxins from eating junk foods. And since Chiri is nowhere to be seen after Nozomu drowned in the hot springs, we can assume that Kafuka is possessing her.
The outro for the first season has Nozomu chasing Kafuka on a boat crossing the Sanzu river (think Japanese Styx), hinting that she already left the living world.
Not to mention that the first season's intro and outro have the girls' faces concealed or looking away.
Also, in the manga, no single panel shows all of the girls at once, since Kafuka has to actively replace one of them. When she appears, one of the girls that was previously present would inexplicably vanish from subsequent panels.
In the manga, when Kafuka paints for the sake of it, she paints a very detailed car accident, the same accident that took her life.
Abiru mentions in the manga that she got her eye transplant from someone who died in a car accident.
The line early in the series "A meeting that was never meant to happen" about Nozomu and Kafuka takes a more darker meaning given Kafuka was supposed to be dead by then.
It may well just be that Kafuka's eyes are made to creep you out.
When Chiri is reading the book that identifies future crimes based on laughter, Nozomu's first laugh indicates that he will commit marriage fraud. In the finale he repeatedly marries and divorces his entire class to remain with Kafuka. One of his brides is an illegal immigrant.
Nozomu doesn't realize his next door neighbor is actually Kafuka in disguise. You would think he would pick up on it after a while, but he doesn't, because his neighbor is being possessed by Kafuka, just like the rest of the girls. The reason that Nozomu doesn't recognize that she's Kafuka is because she ISN'T, at least some of the time. He probably actually does have a nice college student neighbor that just so happens to be a part of the Hive Mind.
"Zetsubou Yuugi" (lit. Games of Despair), by Kenji Ootsuki and the Despair Girls seems to be a random love song. The singer explains how love is like "Hide or Seek" or "Tag", and how he isn't certain who will be "it". Meanwhile, various voices (including Kafuka's) insist that they're present and willing to love the singer, but are "going to run away". The singer someone "pictured in [his] mind" but can't make out who. It seems like a weird metaphor, but it makes perfect sense if you remember that Kafuka is a body hopper, and her appearance is just a hallucination. Whoever she is possessing is "it", and Nozomu has to find her. She's pictured in his mind, but he can't make out who she is because she's a hallucination. Fun side note! With this interpretation, the song is actually a duet!
Past Chapter 150, Kafuka starts becoming Out of Focus. Along with the reveal that she's been dead all along, the last chapter reveals that Kafuka's friends will eventually forget about her.
Sayonara, Zetsubou-Sensei is pretty blatant and tries to cross the line twice, but when Maria (the very young and naive but wonderfully Polyannaish immigrant) sees someone about to molest a child, she believes that he's just being a nice guy to children. Refuge in Audacity, right? And then you realize why everybody wants to protect her. This then makes the horror even more on-target, when you realise that the girl who is constantly hit on by the recurring pedophile is non other than Meru Otonashi, the local Shrinking Violet. And yet, everyone hates her guts because of her abusive e-mails, and on several occasions, she is made the butt of physical abuse or violence. In other words, they don't care if she gets molested, because they dislike her.
With the revelation in the manga that Kafuka was Dead All Along, this puts up the disturbing thought that every time Kafuka appeared, she was actively possessing one of the girls in the class without anybody realizing. This also means that since the viewer can also see Kafuka, by extension you have a piece of Kafuka inside you as well!
"Which Kafuka are you?"
Nozomu once had a dream where everybody is the opposite of his/her real life self (for example, Usui is cool and popular and Kafuka is pessimistic). In that case, it is possible that Abiru, an alleged victim of DV, is an actual victim of DV in the dream.
But it's okay though, it was all a dream.
In Chapter 146, the main cast gets possesed by annoyed animals, who are frustrated because the forest lacks food, their home (dam) has been destroyed or isn't finished yet, and they plan to use the girls' bodies to do the labour. Kafuka is the only one not possessed. Because she's already possessed. Kind of.
Concerning the Kafuka hivemind, there's a theory going around that Maria came across one of Kafuka's organs because she was really hungry...
In one instance, Kafuka comments that her father is such a kind and protective father because he insured her life. Becomes Fridge Horror when you remember at the start of the series, she also commented (in her own way) that her father got laid off from his job and often tried to commit suicide. Put two on two together... especially with The Reveal.
At one point, Chiri accidentally stabs Nozomu, believing it to be some guy walking down the street. Aside from the horror of a young girl attempting to kill a man in public, with hundreds of potential witnesses, the guy she mistook him for was black. You may think I'm being overly sensitive, but in Japan, there are... really, very few black people, and Chiri has literally no social contacts outside of her classroom, so her knowing anyone who's not Japanese (except Keare... sometimes) is incredibly unlikely. This means that she either did know the person and wanted him dead for a reason, which is very unlikely, or she stabbed him because he was black, which seems more obvious, especially from a person like Chiri. And considering how Japan allocates very ridiculousstereotypes to black people from anime and western comics, Chiri would stab him, because Chiri thinks that not conforming to these stereotypes would be seen as unorderly and untidy... well, that mindset is what makesChiriChiri. This sheds a whole new light on Chiri's troubled psyche, and even then, it's still almost nothing compared to Kafuka's, which adds another layer of terrifyingness to the manga that's hard to spot.
Jun Kudou was rejected by his very traditional Japanese/Christian family for having a blood transfusion. He's also very obviously smitten by his male teacher, like the female cast. Think about that for a second.
Chie says that every girl will eventually forget about Kafuka, and any of her action will be remembered as one of the girl's action. However, this would raise suspicion when you realize that some of the girls she possessed (like Mayo or Kaga) would have acted very out of character.
Well, Kaga has mentioned that sometimes she suffers from drastic Mood changes sometimes feeling really happy and others feeling even more depresed than (to her) normal, while it at first it may seem as kaga suffering from Bipolar affective disorder(A.K.A being Maniac-Depresive) it could also being that her highs are she being possesed by Kafuka and her lows being possesed by one of the girls from the showa period who commited suicide.