Just finished up the mass guessing.
Theories I find plausible (don't read ahead if you dislike spoilers):
1. Madotsuki is a serial killer.
She's not a hikkikomori. She's under house arrest. The dream characters and places represent her victims or aspects of her insanity.
The Toriningen are her murderous urges. The Lunatics send her to an inescapable room—allegorical for how giving into her insanity landed her under house arrest.
Monoko was the first of her victims—a little girl Madotsuki babysat and brutally murdered and mutilated. The fact that she's perfectly normal until Madotsuki uses the stoplight effect on her symbolizes that she was the weakest of Madotsuki's victims—she had tried to run, but all it took was for Madotsuki to say "Stop", and her fate was sealed.
Monoe was Monoko's older sister and a former classmate of Madotsuki's. She was the only one who knew who killed her little sister, so she had to die as well. She teleports Madotsuki away because she doesn't want her killer anywhere near her.
Masada was Madotsuki's piano teacher, who she was very close to and eventually developed a crush on. When he rejected her advances, she decided If I Cant Have You and killed him.
Poniko was her most recent victim, and the one Madotsuki feels most guilty over. The two were the best of friends in the past, but Poniko grew distant and started ignoring Madotsuki. At this point, Madotsuki had figured out that her victims were appearing in her dreams, and so killed Poniko in order to keep her forever.
Uboa represents Death. He periodically appears in Poniko's place to remind Madotsuki that, although her victims may be alive and (relatively) well in this world, they're still dead at Madotsuki's hands in the real world.
The Number World and Block World both represent prison. The Number World normally has small, one-digit numbers (years in her various sentences, perhaps?), but also a few absurdly long numbers (prisoner numbers?). The blocks, obviously, are cells/cellblocks.
Madotsuki's killings generally happened on winter (Snow World) nights (Dark World/Candle World), and, of course, the most frequent weapon was a knife.
The Cat effect symbolizes that all of Madotsuki's victims were close to her. A child she babysat, a classmate, a teacher, a friend. Never strangers.
stuffai-san (the corpse you get the Stoplight effect from) might be another victim, or just a symbol of what Madotsuki did with the bodies of her victims—left them in the middle of the road in order to make it look like they had been hit by a car.
Madotsuki's Self Delete is her atonement for her killings. Either that, or she wishes to "join" her victims and be with them without the guilt of being the reason for their deaths.
2. Something even worse than the dreams is going on in the real world
The evidence is Madotsuki's reaction if you try to open the door in the real world - she shakes her head. It seems that she has no trouble with any of the creepy inhabitants of her dreams, but she doesn't want to face whatever's going on in the real world.
And note that the TV in her (real-world) room shows nothing but a test pattern. What is happening with all the transmitters in the world? This Troper believes that the game takes place After The End, where most of Earth has been destroyed by some terrible cataclysm, and Madotsuki does not want to live in a barren, barely inhabited world. She does not leave her room because of what's beyond the door - the horribly charred corpses of her family, a horde of zombies, etc.
Notice also the rather barren-looking landscape that is visible from the balcony.
And the fact that there is no building behind her balcony? The entire building- some kind of tower if the view is to be believed- is no wider than her room. That's just wrong.
3. Uboa looks like Che Guevara
Well, in some art anyway.
4. Masada and Uboa used to be the same.
Twins, Separated At Birth, two aspects of the same being, maybe even Comedy and Tragedy. They look sort of similar, the face scheme anyway, but act in different but possibly related ways. Uboa stands there and never does anything to harm the player; all he does is transport you to a nightmare realm you can't escape without waking, and his happysad expression falls and becomes completely sad if you touch him and get transported there. He could just want a hug, but is too afraid to hug Madotsuki in case he transports her to the other realm like he does everyone else, and can't do otherwise. Masada runs from you if you have the knife equipped, but other than that he seems to be a nice, if shy person. It's difficult to tell with the lack of dialog. Uboa doesn't seem to be much different, except that his mask (if it is a mask) covers his whole body (perhaps in hopes that it can keep people from being transported if they only touch the mask?) The differences could be that Uboa is used to hurting (or at least inconveniencing) anyone who gets close, and Masada may be used to being hurt, or, after being separated from Uboa, having his one defense taken away (even if it did stop anyone getting close). (Oh, yeah, this also goes with the perfectly sane and not at all wild guess that Uboa isn't evil. This Troper just sees sad, and never would have guessed that Uboa was thought to be malevolent if not for TV Tropes.)
Uboa and Masada are the same. They "both" raped Madotsuki.
5. All the dream worlds are distorted representations of places and things she knows in her real life.
The Forest World is a road she usually travels by bus, the Block World is her school, the White Desert is the first complex dream-world she ever developed and is based on her childhood doodles and pen-drawings (white paper, black ink, nothing else), the Neon World is a video arcade, the numbers world is a train or subway station, and so on. (I haven't played it in awhile, that's all I remember immediately.)
I think the subway world is the subway system- note the vague people that do some sort of dance in the background while you walk- and that the numbers world is her opinion of computers or mathematics- but yeah, this works pretty well...
6. Almost all the characters are friends/acquaintances of Madotsuki. (And she also had a really crappy childhood.)
Building upon some of the other WM Gs above, and said elsewhere...
Monoko is (Or represents) one of her first friends. She was killed in front of Madotsuki's eyes when they were playing near a traffic light, and she got hit by a truck. Being young, Madotsuki didn't really understand what she saw, hence why Monoko is represented as a mutated girl, rather than a mangled corpse. Madotsuki feels guilty over this, and blames herself a fair bit.
Monoe was another friend of hers who drifted away. Either she moved, or simply made other friends, hence why she fades away.
Masada was her music teacher with a lazy eye. while all the other students mocked him, she enjoyed him and his classes. Perhaps she learned to really harness her imagination with him, telling her about various books that really opened her eyes. Presumably, he got transferred to another school.
Any explanation for why he runs from you if you have the knife, then?
The original teacher was always quite shy, and a bit nervous and cowardly. Perhaps he wasn't transferred as much as quit after being threatened by a student in an act that stuck in Madotsuki's mind.
Toriningen are how Madotsuki saw other girls. Being short for her age, she saw them all as tall, and bizarre looking with their makeup and weird hairstyles, clucking away about things she didn't understand. Either they ignored her (And had fun without her, hence the Toriningen picnic she can't get to) or they mocked and bullied her, hence the psycho Toriningen.
What about the friendly Toriningen in the Numbers World?
Those fit under 'ignoring her.' Those Toriningen don't actually help her, they just leave her alone. it's not like every girl in school picked on Madotsuki. Hence why some are just weird looking, while some are malicious. As for the Toriningen in the department store who changes your menu, I'd say that represents one time when she recognized a girl that picked on her at school working at a store she was shopping at with her parents one day. The dissonance between this girl she thought was nasty, and seeing them be a polite server, made her confused.
Now, the big one. Poniko was the last friend Madotsuki had. Poniko seemed to be a kindred spirit, somebody who didn't talk much and didn't have any friends. Indeed, it wasn't much of a friendship, as Madotsuki simply hung around Poniko, but Poniko mostly took advantage of, if not completely ignoring, her. Still, Madotsuki, emotionally repressed as she was, thought it was a friendship.
This all changed after months, or years, of this supposed friendship. What happened? Poniko raped, or tried to rape, Madotsuki. This is where Uboa comes in, representing how that girl Madotsuki thought she knew very well became a monster. Madotsuki tried to defend herself, and ended up grabbing a knife, killing Poniko. Utterly horrified at having who she thought was a friend attack her, yet also killing her, sent her over the edge, and she became a shut-in.
Or maybe Madotsuki got too close or clingy and Poniko (perhaps callously) told her to back off. Madotsuki, already sensitive from loneliness, takes this the worst way. After all, Uboa will transport Madotsuki if she just runs into Uboa: the knife isn't required.
That works quite well, actually. I suppose I was just trying to find a reason for the knife and all the supposed loveual imagery. But just being told to eff off by one you thought was a friend would be devastating to somebody as screwed up as Madotsuki. (As one Troper above said, who says she's completely innocent amid all this? The gal's messed up.)
tvtropes is a pretty cool site
