Alt-timeline was clarified in Sundown by Jackob

I believe that Sundown was the most relevant episode of season 6 so far because it did the best to show that the alt-timeline directly affects the island-timeline (or vice-versa). I think that is why the writers have said that they are running parallel to each other. It's not that one is happening and the other has yet to happen (or has already happened), but that they are both happening at the same time.

There has been signs of this in previous episodes (mostly Juliet saying "it worked" and apparently having a flash of sorts asking Sawyer for some "coffee"), but this episode did the best to thematically express to the viewers that they are affecting each other (much like how the flashbacks affected the normal-timeline in season 1 + 2).

First, the episode starts out with alt-Sayid being questionable, he is mysterious. What was he doing all those years when he was away from Nadia?? On the island, Sayid is also mysterious. Is he fully evil or is he salvageable yet?? I think that is why Dogen tested him (just like Omar seemed to test Sayid in requesting Sayid kill the people after him...Sayid says "I am not that man anymore", hinting that he is trying to salvage himself in the alt, but will he be strong enough?). The same questions you should be asking yourself in the alt, are the same questions asked in the normal-timeline. When Sayid eventually kills Dogen and Lennon and fully embraces Locke's side, we see in the alt Sayid reverting to a self that he swore he was done with, a darker side of himself (killing Keamy's team).

Dogen's speech is also relevant. Jacob promised that if he came back to the island, he might someday be able to see his kids again. I think Jacob was telling the truth, and now that Dogen is dead, the only version of himself is the 2004 version, thus he's reunited with his kid. If you redeem yourself on the island, you change the course of your life in your alt-life (or "real life", since it's the only one left when you die) for the better.

So now we can go back and analyze the importance of the last few episodes.

What Kate Does: Kate is still running from the law, but she tells Claire "Would you believe me if I said I was innocent", and I think, at this point, we gotta figure she IS innocent (still hasn't been corrupted by the MIB), but I think if it turns out that she gets corrupted on the island, we will find out that either a.) she DID kill somebody and was lying to Claire or b.) she DOES kill somebody, possibly significant, in a future alt-episode.

The Substitute: Off the island John Locke comes to terms with himself that he isn't a hunter. He can't walk. He has to get over this fact and accept that being a substitute would be in his best interest. He lets go of his drive to "be better" and settles with the fact that he is in a wheel chair and there is nothing he can do about it. On the Island, MIB shows glimpses of John Locke ("Don't tell me what I can't do!") and I think deep down, there is a little John Locke still in there. But since Locke "settled" for the substitute, he is stuck as the MIB. The only way I can see him having more of an effect directly on the MIB (maybe even overcoming him entirely) is to call Jack, have his spine fixed, and once he realizes that he IS a hunter, he might have to do something drastic....and yes I mean "You have to die John". In this way, Locke in the alt (along with the help of "Jackob") could be the most significant of the "alties".

Lighthouse: This one is fairly straight forward. Jack redeems himself in the alt-timeline, showing no hint of "evil", so in a way, so far, he is the best candidate to take Jacob's position. His alt-timeline may have been affected if Jack chose a different route (ie. turning to MIB's side instead of Hurley's). I think that as long as Jack is on his route to salvation ON the island, he will have a happy, redeemable alt-reality with no signs of his past self bleeding through (no drinking/fatherly problems).

So what does this leave for the rest of the characters?? Well I believe that we will find out that Sawyer is already corrupted by the darkside (Flock's power of persuasion is immense and unbearable...thus his ambiguous questions he proposes to both Sayid and Sawyer...I bet he did the same to Claire promising Aaron). So for Sawyer's episode, I see him being corrupted to the darkside both ON the island AND in the alt much like Sayid's episode. I think that we will find out that Claire did something very bad in the alt-timeline to get her to where she is now (on the darkside). Maybe she killed someone...maybe she pulled the plug on her dying mother for selfish reasons??