The Book of Eli/WMG

Eli has a Pip-Boy, or something similar.

The Vaulttech Assisted Targeting System lets him pull of so many improbably badass moves while taking minimal damage. When he was brought before Carnegie and shot, he was out of Action Points.
- Which is strange, because by then you would have thought that he'd be at least level twenty, which means he should have had Grim Reaper's Sprint.

Eli's "voice" that told him to go west was really a radio broadcast.

He knows where the "safe place" is right away. It's possible that he was trying to make it relate to Solara, who obviously wouldn't know what a radio or Alcatraz is.
- But how would a radio broadcast know where to find a Bible under a stray pile of rubble?
  - Easy. He could have heard the radio broadcast and happened upon the Bible by chance while investigating it.
    - Didn't the voice tell him where to find it?
    - From memory, it led him to the Bible, and told him where to put it.
- He said specifically that he heard it in his head even knowing that it would make him sound crazy. That does not point to it being a radio. Besides, she knows what an ipod is, what headphones are, why wouldn't she know about radio.
Just in keeping with the apparent Fallout theme, I'm going to say it was Three Dog. Because he knows everything.

The men on Alcatraz are a benevolent Enclave.

Instead of trying to genocide everyone in the wasteland, they're simply trying to preserve what they can find until they can make ground and begin teaching the wastelanders. Note that they look cleaner and seem more official than any normal wastelander (note the man who first points his rifle at Eli and Solara and the commands he shouts, and the other guards' uniforms).
- That sounds more like the Brotherhood of Steel, minus the militarism.
- No. West Coast Brotherhood of Steel have no interest in ruling the wastes or spreading knowledge, and they didn't have an offshore base.

The Flash is really what happened after the events of Unthinkable

Either the three-to-four nuklear bombs were enough to to make America a barren wasteland, or that the bombs just increased the heat on the war.

Solara is the Dragon's daughter

Explains why he wants Solara in exchange for finding Eli, why during the standoff he actually says 'please' to Eli, and why he looked so surprised when Solara indirectly kills him.

Eli is not actually blind

Instead he's legally blind, only able to see short distances and make out basic shapes. This means that he can't see well enough to read a normal book, but he can see attacks coming and his spatial awareness is attuned to the point where it and his other senses are able to make up for his impaired vision. This also explains why he doesn't see Alcatraz until Solara points it out on the sea.
- This explains why he jumps at the sight of the dead body in the room- he can tell it's a dead body.
- It's entirely possible he flinched because of the SMELL, not the sight.
Alternatively, he has blindsight. That is, he can see, but he isn't consciously aware that he can see. Yes, its a real thing. It would explain how he can hit targets that are quite far away as well as why his eyes track movements nearby.

The old couple are Muriel and Eustace Bagge

That's their house...I mean, it's creepy. The windmill is the same too. Courage must have either died in the flash, or had died before.
- I'm now accepting this as canon.
  - He's back on the moon with his birth parents, and now leads the Dog colony.

The old couple probably had at least one Bible in their house

I mean, they have a working phonograph, dishes, and all in all their house seems to have everything from before the Flash. Given how common Bibles are, it wouldn't surprise me one bit if they had the book Carnegie was looking for, in a format he could read. Dramatic Irony much?
- They eat other people and listen to Anita Ward. It's definitely a modern interpretation of the Bible.
  - Ahem... "This is my body/blood whenever you eat/drink it do this for the remembrance of me". The old folks just twisted it around a little.

The Book of Eli is loosely based on someone's play through of Fallout 3.

It would make sense. Maybe some details were changed, such as the reason why people were trying to kill Eli. Maybe they were mercenaries that were just given a story after Eli disabled the bomb in Megaton. The person simply has a mod that gave a bible to his character. Of course, the ending would be completely made up, possibly after the person had to drop their bible for some reason or another.
- Garry Whitta, the screenwriter of Book of Eli, was the Editor in Chief of PC Gamer in the 90s. i wouldn't put it past him to have played Fallout 3.
  - Note that there were two/three games (depending on how you count it) preceding Fallout 3, plus the original Wasteland-- It seems likely that someone involved with the movie's look/atmosphere played one or more of said games, but considering that Eli began production a year before 3 was released it seems more likely that the movie was influenced by one of the older games.

The film is set in the universe of A Canticle for Leibowitz

It takes place before or during The Simplification. Either Alcatraz was eventually destroyed, or it managed to stay secret until after the first and second parts of A Canticle for Leibowitz.

It's actually a horror movie, with Eli as the tool of an evil God.

Christianity and/or Jehovah did start the war. Afterward, people did their best to wipe out the poisonous meme, destroying all the copies they could get their hands on... but one last carrier of The Virus managed to get through and start the infection all over again.

Eli's iPod has an audiobook of the Bible.