The Road/WMG

The boy doesn't exist.
The boy is just a hallucination spurred on by the man needing a reason to live. When Ely asks "Are you a little boy?", he's only thinking that because the man was talking to someone else. Notice Ely never talks directly to the boy, or vice-versa.

Conversely, the father doesn't exist.
Or rather the father was dead at the start of the novel. The father is a mental construct/hallucination of the boy, helping him deal with living in a post-apocalyptic wasteland. Anytime something "bad" happens like stealing, killing, and so on, it's the father that does it. In reality, the boy is doing everything, but he imagines the father is doing these bad things to help him retain his grip on his humanity.

The Road is a sequel to the film Idiocracy.
Not much to add to this one. This theory showed up over at The Onion AV Club and demanded to be shared.

Everyone really is Jesus in Purgatory.
So there's an unspecified disaster that happened at some point before the book starts. It killed off trees, animals, cockroaches, sarcastic pimp-bots that look like Jude Law -- and yet somehow a handful of humans lived through it. This is a huge clue that we're not supposed to take this as literally After The End; all the human characters are actually dead. The boy is actually an angel and he is helping the father ascend to Heaven (remember all that business about "carrying the light"). The father's death was actually his ascension, and the angel/boy will go on to save the people who show up at the very end.

Yellowstone caldera is the cause of the cataclysm
yellow stone (or any supervolcano for that matter)is a good fit. it won't just effect America but it's capable of covering the WHOLE planet in dust and debris for years if not decades. that's long enough to starve the planet of sunlight, thus decimating vegetation and wild life.
 * The main flaw is that, well, we actually do have something of an 'upper limit' known for a Yellowstone eruption (and for the rest of the supervolcano), and they wouldn't make things quite this bleak, world-wide... but Yellowstone can still work, though: the story takes place in North America, and the rest of the planet would very likely be in no shape to send help to any surviving Americans, what with needing to work hard to keep some semblance of civilization running during the years without summer.

Aliens have detonated a biological warhead to choke the planet to death, planning to terraform Earth after the indigenous life dies off
Perhaps the warhead hit in the eastern hemisphere, thus North America only hearing the detonations and feeling the effects. Maybe the Aliens are already hard at work on the opposite side of the planet. Either way, the hopeful ending at the end of the book is in vain.

The cataclysm turned North America into No Man's Land
This is related to the Yellowstone theory, except that the rest of the world fares (relatively) better. Realizing that there's a snowball's chance in Hell of expecting survivors, the remaining nations cordoned off the continent. Apart from pointing satellites on the ruins, they're just waiting for the dust to finally settle.

The Planet is actually a partially glassed UNSC Colony
Similar to the above alien theory, This planet was a earth colony that got abandoned after the UNSC withdrew leaving the rest to die a slow and painful death along with the planet. Maybe it wasn't glassing perse' but maybe a Type of Depopulation Bomb. The Covenant didn't have time (or the resources after a previous battle) to glass it so they sloppily used another weapon and left.

They are "carrying the light"
They're too lucky. Unoccupied bomb shelter? Abandoned beached yacht? And then the man dies and the boy is immediately rescued by the only other decent people ever? God has a plan for them. Or something.
 * Remember though, the other decent people had been following them for a while. They would've rescued him whenever the man died.

The world isn't all dead.
I mean, they travel across half of America, but there's more to Earth than just that. Africa? South America? Antartica? The Marianas Trench? I mean, the author keeps most of the book feasible, so I wouldn't be surprised if Greenland or Australia would have taken a pass. America (and likely China and most other major world superpowers) just got royally screwed with the crap end of the stick. That said, it wouldn't make the novel any less post-apocalyptic and depressing, as the boy probably won't ever hear of any surviving patches of Earth, even if they DID exist.

Man and Woman were anticipating the cataclysm
Notice in the beginning they had tons of can goods. Then there was the Robert Duvall character saying "They said this would happen". Then there's that bunker were it looked like it might have been stocked in preparation of the impending cataclysm.

The family eventually ate their horse
Exactly What It Says on the Tin.

The Book of Eli takes place in the same universe
The bad thing that happened is pretty similar - but the worst was over by then, and the west fared better than the east.
 * Ely is Eli.
 * I don't know, The Book of Eli was pretty explicit about taking place in a post nuclear apocalypse. Also I'm no expert on this, but if this post apocalyptic world has the worst thing on the West Coast being San Francisco's impressive lack of fog while the East Coast is a barren hell of ash and death then I think there's something seriously wrong.

Take Shelter is a prequel to The Road.
The prophesied unknown horrible storm is whatever happened to the world.