OK you guise, I have some long-winded brainfodder! First of all, I've been obsessed with this game ever since I first came across it on wikipedia. It's probably one of the greatest games EVER, I love the creeps, the music, the general feel, and most of all the MYSTERY!
I think all the black/white characters are dead. Madotsuki's somehow connected with all these deaths, whether they are people she knew well prior to their death or happened or they were just passing faces, they made a great impression on her mind by dying.
Thus my theory is that Uboa/Poniko was someone really close to her, whose death was a big shock. She's in denial, so when Poniko first appears it's how she remembers her, then when Uboa comes out it's probably a flash-back to the shock she felt when she saw/learned of Poniko's death. Another theory that supports this idea of mine is that Poniko's face was somehow disfigured (into that creepylicious grin), and when Uboa's stabbed and the face changes, it might be a reference to how Poniko's face had been restored (to almost non-existence) for her funeral.
Monoko and Monoe (who I'm certain are two different people) either were her school mates, who died during Madotsuki's stay in school or people she's seen pictures of and heard of. Monoko's graphic appearance may be a figment of Madotsuki's imagination from hearing stories of her death (she probably never really saw her post-mortem), so that's why she has extra appendages in place of blood and broken bones. If she had witnessed her die the impression would have been much more graphic. Monoe died without any visible physical symptoms (therefore the peaceful creepy grin, like a school portrait at her funeral).. Masaki-san, probably dead too, but I haven't really figured much from his appearance.. The preggo lady/decapitated preggo lady is probably a result of witnessing/hearing stories of some accident who another person she knew suffered. This particular person probably had a post-mortem c-section, thus the gaping stomach-mouth thing..
The only person who doesn't fit into this theory is Shitai-san. The reason Poniko is in colour is that she was someone who really mattered to Madotsuki, and she spent a lot of time with, thus she also has a room to herself within the dreamworld.
The effects are things that Madotsuki hated about herself/envied in others. Long hair, blonde, poopy hair, fat, midget, "towel" = poor health.. the Toriningen are most likely people who tormented her, same as the faceless girls by the lake are girls who didn't help or pay her any attention whilst she was being picked on..
Um.. maybe she was driven to staying in her room because of the shock she suffered from Poniko's death (also the reason she kills herself in the end), on top of her being bullied. Poniko was her only friend? Maybe lesbian lover? I'm pretty sure she's not being abused by family or anyone she lives with because how does she eat/clean herself/go to the toilet. She's probably decided by the time of the game's beginning that she's going to end it all, and doesn't want to leave her room so she won't be discouraged. :(
And that's all for now folks.