In the four years since the series started, fan sites have sprung up focusing on the show, and fan theories to explain the mysteries are everywhere -- many now thoroughly debunked. But I think I've found the most comprehensive, well-illustrated, and plausible theory yet: Jason Hunter's Lost: A Theory on Time Travel. Warning: don't read it unless you're caught up on the show -- it contains all sorts of spoilerish information, including updates related to last night's episode. Hunter also includes speculation about what might happen in the show's future (if his theory is correct), but he doesn't seem to have inside information.
Hunter's theory takes many, many pages to explain (including graphs!), so I'll just give you a taste of a few of his rules related to time travel:
1. When someone enters the time machine, they can only go back in time - and only to a time where the machine was currently running. 2. When you go back in time, you do not de-age. For example, if you are 50, and go back 10 years in time, you do NOT have your 40-year-old body. HOWEVER, while you are re-living 10 years of your life, you body will not age until you catch up with the time in which you entered the time machine. ... 5. If you go back in time and die, you are not "totally" dead because there has already been a variation of the universe where you were alive in the future. Thus, you become "half dead" until time catches back up. In other words, your presence may be known to some people but not others. Your presence would only be known when you are required to make an impact to fate.
LOST returns in two weeks with its two-hour season finale. After that we've only got 34 more hours of TV (two more seasons) to wrap this thing up! If you've got a nutty theory, please share in the comments. (Or just start your own website like Mr. Hunter.)