This post is going to go over what happened on the season 5 finale of Lost, so if you haven't seen it, don't read this until you have seen it.
.:!SPOILERS ABOUND!:..:!SPOILERS ABOUND!:..:!SPOILERS ABOUND!:.
First of all, that wasn't Jacob that was visiting everybody.
Surely that's obvious, yes?
It was whoever that guy was that wanted to kill Jacob at the beginning of the episode. If you didn't come to that conclusion and are balking at my logic, or asking "Then why did he take the form of Jacob? It's not like they would recognize or see him later." let me explain.
Firstly, it would destroy the surprise if it was that other guy, so it couldn't be him for the audience's sake. Secondly, he can obviously change forms and wanted to hide his identity at all costs. The most important reason, he was selecting them to set his plan in motion: that of killing Jacob. By going and talking to all of the original survivors he altered their paths to all meet on Oceanic Flight 815, which would ultimately crash on the island and set off the chain of events.
I believe the only time we actually see Jacob leave the island is when he talks to the bounty hunter (though that's questionable now) that brought in Sayid. Probably as a matter of insurance in case his 'friend' succeeds in killing him.
It's almost as if Jacob is God, and the other guy is Satan. Satan is desperate for any way to kill God, but God will always prevail no matter what. Which brings me to the next part of my post which will be a bit tough to follow. Unless you're as well versed in time travel theory as I am :)
When the other guy, disguised as Locke, manages to get Jacob killed by way of Ben, he inadvertently de-linearizes (no, that's not a real word) the space time continuum. What I mean by this, is that the continuum is now open to change instead of everything having already happened. Notice how it's not until Jacob is killed that Juliet sets off the hydrogen bomb? Although the group of survivors 30 years in the past are 30 years in the past, once Jacob is killed the time line is open to change.
This allows Juliet to successfully set off the hydrogen bomb, which obviously shouldn't have gone off in the first place as the island would have become completely uninhabitable. This event negates everything that happened on the island and pretty much causes a hard reset of time. Think of it as a computer crashing, and resetting to a previous, safe state.
The other guy might have found a loophole, but in using it he destroyed it. Totally something God/Jacob would bank on :)
I believe this is all true because the super quick shot of the eye at the end is Juliet's. She's okay, and I'm going to assume everybody else is as well.
January just cannot come soon enough.