Eh, got too tired to think more about my theory so posting the incomplete version. I picked up bits and pieces from stuff people have talked about elsewhere.
http://i.imgur.com/YQwIwo7.jpgWhy did Munakata refer to Asahina and Naegi as despair? Because everyone is latent despair, and they're being converted to despair one by one before committing suicide. So Munakata reasons that it's easier to kill them before they inevitably submit to despair.
Look at the death scenes (refer to image above). The anime goes out of its way to point out the Monokuma screen above each dead body. Because the mastermind needs some way to visually communicate with the participants, via the brainwashing techniques that Ryota has perfected. After everyone falls asleep, one person is revived and is brainwashed into becoming despair, after which they commit suicide.
There are a lot of small details which support this. Gozu's eyes being gouged out; maybe he tried to stop himself from looking at the video? Ruruka trying to kill herself with candy like the way she killed her two best friends, and slicing herself across the legs like Nagito did, maybe to try to snap her out of the brainwashing. The ripped pieces of cloth in Ruruka's hands. Ruruka and Chisa crying as they died, implying they were awake; if the killer was someone else, why would they be awake? Because it was a suicide. The knives are probably hidden around the building or are provided by an accomplice who also sneaks around at night through the ceiling tiles.
The bodies are suspended because Monaca was messing with everyone. This is also why Ruruka's body isn't suspended; Monaca left.
So who set this up? Recall that Tengan wasn't too worried about dying off, and he also knew the attacker. Why? Because he is one of the people who set up the game. After the disaster of Class 77 becoming despair and the failure of Izuru, Tengan realized that the Hope can only be instilled if people have already overcome despair, so they won't be susceptible to it. Tengan already sees that Munakata and the rest of the FF are on the verge of despair, so he decides to put his plan into motion to purge the current FF of despair. With the help of Ryota, he sets his plan into motion: members of the FF will be plunged into despair one by one to see if they can overcome it with hope. If not, they kill themselves and the cycle continues until they find someone who can become true hope. This what Tengan meant by not letting the results of the Kamakura project go to waste. It's why he knew who the attacker was. It's how this entire game could have been set up under the FF headquarters without anyone else knowing. It's why he entrusted the world's hope to Ryota in his dying message, to make sure the game continued to run smoothly. It's why Munakata went nuclear after Tengan told him the truth, and why he's killing everyone before they fall into despair, because Munakata believes only he is true hope. It's why Tengan was surprised when Munakata killed him and asked Munakata where he would find hope.
Also, as I said above, Kyoko's notebook moved during sleepy poison gas time, which means someone in the room was awake during that time (closed room, although technically we still haven't seen if it's still closed). This supports Ryota being some sort of accomplice, since other than the theory that Kirigiri was faking her death, I don't see anyone in that room who could have looked at the notebook.
