After my last theory was completely shattered in the very first scene of the season finale, I'm not going to make theories anymore. From now on I'll only consider "what if" scenarios.
Anyway, here's a couple:
What if Jacob is THE Jacob and Adam and Eve are THE Adam and Eve and Lost is one big, 6 year long advertisement for some church?
What if the bomb was like the nuke that Sideshow Bob stole in The Simpsons when he was trying to get rid of television? When he detonated it, it shows what appears to be a a devastating explosion then cuts to commercial. But when the show returns, the explosion is seen as only a couple feet high due to the amount of time it went unused. What if the season 6 premier starts with a mushroom cloud and the camera zooms out to show the cloud only being about as big as a beach ball?