I've never posted a theory, so if this has been explored and refuted, please excuse me.
Okay, so now I think that Jacob is/was some sort of Guardian of Time and/or Space. At the end of the episode 'The Constant', Daniel is flipping though his journal and turns past this page: http://images1.wikia.nocookie.net/lostpedia/images/6/64/Dan_journal_6.jpg
It appears evident that what happens to our Losties when they 'flash through time' is that their conscience travels between 'Real Time', 'Imaginary Time', 'Space Time' and 'Imaginary Space'. Never having taken any physics classes, I'm not exactly sure of the difference between Space & Time (time to read!), but I surmise that each of these has its own reality.
Now, I think when Jacob says to 'Man in Black', "They are coming", he means that without him doing his duty, 'guarding space and time', the realities will all collide. What the consequences of that are, we'll find out . I'm not sure if MIB fully understood the consequences of his actions, though, for he seemed a bit taken aback when Jacob tells him this.
Maybe, when you die in one reality, you live on in the other. This is why I think we may see George Minkowski (Fisher Stavens) & Charlotte Lewis again.
Also, I found this when I searched 'guardian of time' on google: http://en.wikipedia.org/wiki/Guardians_of_Time_Trilogy. I'm sure it has nothing to do with the show (especially since the first book came out two years before), but there are some eerie similarities between them.
Anyway, I wanted to get that off my chest. Carry on.