Deadman Wonderland/WMG

Shiro is Ganta's sister.
Either biological or adopted.

Deadman Wonderland is an SCP Containment site
The prisoners are D-Class. The candy? Its SCP-500. Also, the entire park is built to contain the being responsible for The Devastation of Tokyo Or as it is better known Prisoner 682 (The Dharma Initiative may or may not be involved.)

The Director is Shiro and/or Ganta's father/grandfather.
Why else would they have the same unitard and extensive surgical scars?

The Director is the anonymous bettor at the Carnival Corpse matches.
He's keeping an eye on his son/grandson and his "organ donors."

Ganta's mother is the anonymous bettor at the Carnival Corpse matches.
Just because Ganta's been living as an orphan dosen't mean his biological parents are dead. However, it's also possible that...

Ganta's mother was killed/committed suicide just before/during The Great Tokyo Earthquake.
In the flashback at the beginning of the manga she's seen playing the piano and crying, because she knows that the Applied Phlebotinum is about to react and cause both the earthquake and a whole lot of trouble for some soon-to-be superhumans. She probably feels that the approaching disaster is her fault, much like Dr. Hineman from Minority Report feels responsible for imprisoning the precogs.

Shiro and the Director are the recipients of the forfeited organs of the Carneval Corpse losers.
Just look at all those scars! The two haven't displayed their powers because The Director is bedridden while Shiro---

Shiro is not a Deadman, she's something else.
If she did have "Branch of Sin" powers either naturally or implanted via the Blood Diamonds or transferred from the harvested organs, they would have manifested during the Dog Race when she was being Ganta's human shield; also, Shiro seems to have made a guard tower which did not appear to have any explosives inside blow up. BoS powers are edge/point weapons: Senji and Minatsuki use them as blades, Ganta as bullets. There hasn't been any scene yet where they're used as explosives. Still, perhaps--
 * Nagi's Owl's Eyeballs explode. Seen here. So Shiro could very well be a Deadman with an explosive move.
 * Shiro is the Red Man. The Red Man is a Deadman. By way of the transitive property, Shiro is a Deadman.
 * Completely Jossed in the last two chapters, where she uses Deadman powers while not being the Red Man.
 * Shiro's Branch of Sin didn't activate during the race because until recently, the power was completely tied to her Wretched Egg personality.

There are different aspects to Branch of Sin powers.
The Eat Man guy is proof that BoS powers can be used in ways other then "blood blades/whips/bullets"; besides, we've only seen four Deadmen (out of at least a dozen or a score) use their powers, sooo--

Shiro is a Deadman, she's just never been injured before.
Her powers are never shown "on camera," only the results. It's assumed she lived in the same sort of highly secure area as the Director, or perhaps she's been drugged for a long time and was released to look after Ganta. Since she's never used her powers before, they didn't come out when she got injured during the Dog Race.

Whoever or whatever created the Deadmen is directly responsible for the Tokyo earthquake.
See S-Cry-Ed, Static Shock!, Teenage Mutant Ninja Turtles, etc.

The underlying reason to all of the above is "because it's Seinen".
 * Confirmed.

The warden is actually Shiro and possibly Toto's father
She called the old head of deadmen wonderland grandpa and the original warden was Tamaki's father after all. Toto and Shiro are also both insane albinos that freely wander the prison.

Makina is the (biological or foster) mother of Ganta and Shiro.
http://www.onemanga.com/Deadman_Wonderland/11/02/ That is all.
 * I dunno. The woman in that picture doesn't have Makina's Gag Boobs.

Senji is either a descendant of, or an AU version of, Kenpachi Zaraki
. Both love violence, both seem to be extremely well-built, both have the same spiked-up hair and eyepatch... well, you get the idea.

DW is Superjail
That is all.

Senji's coin is double side
That's how it always comes up lizard side up.

--Confirmed, but only in the Anime. In the OVA, the lizard coin is Domon's, Senji's old boss on the police force. He uses the coin flip to trick Senji into doing the early morning patrol, until Senji snatches the coin and realizes it is double sided.

The court that convicted Ganta is part of whatever conspiracy is going on.
Despite how well set up Ganta was, there are some glaring inconsistencies in the prosecution's case, to the point that no impartial court could have convicted him. Namely, how did he manage to commit this crime? 29 students and one teacher can't hold off one scrawny kid? And what happened to the weapon? Ganta was so injured that he passed out and woke up in the hospital, leaving him no time to hide the weapon, but none was found on him, either. The windows were blown in, indicating forced entry and necessitating that for Ganta to have been responsible, he'd have had to place a bomb outside the window, set it off while he was in the classroom, use the resulting commotion to slice up anyone the bomb left alive, and hide the weapon before he passed out from his own injuries. An impartial court doesn't convict someone simply because they appear to be the only one with access when the means to commit the crime are so obviously lacking. The only conclusion I can draw is that the court is part of the conspiracy, and the media is just eating it up, partly for ratings and partly because they don't want to believe the truth.

Genta ends up a broken, scared and pathetic wuss on the inside.
During the course of the series, Ganta develops a kind of split personality. While on the surface, he seems like such a determinator, inside, however, he remains the same weak and cowardly Ganta he was when he entered Deadman Wonderland, unable to cope with all Deadman Wonderland throws at him.