Jughead- So Jacob has somehow brought all these people to the Island over the years. His plan was to raise two of these people from birth on the Island, grooming them to become his replacement, and then he would pick the best one for the job. Enter Charles and Eloise. This is what Richard means by the fact that they have a very particular process for choosing a leader. Meeting Locke for the first time, hearing that he claims he will eventually be their leader, Richard gets doubts about the plan. These same doubts then begin to plague Jacob, causing him to contemplate abandoning the Charles/Eloise plan.
1961
Cabin Fever- Now Jacob begins to have second thoughts about John.
1973
Cabin Fever- Even though Jacob doesn't have total faith that John will be his replacement, he still wants to keep an eye on him.
1976
The Incident, Part 1- By now Charles and Eloise have started their relationship in opposition to Jacob's wishes. Though he leaves them in charge of his people, he has abandoned them as potential replacements. He has begun his search for the time travelers, one of which will be his successor, and Sawyer is the first one he finds.
1977
The Incident, Part 2- Jacob knows the time travelers plan didn't work, but he doesn't tell Richard this. He continues in the dark about Jacob's true plans until the end.
1988
The Variable- Eloise has left the Island leaving Charles in charge. She has become committed to the idea that the future can't be changed, and plays into that plan exactly.
1993
Dead is Dead- Ben becomes the leader of the Others. Jacob OKs this because he isn't interested in his on the Island project anymore, placing all his hopes in his growing list of touched Candidates.
1996
Flashes Before Your Eyes- Going with the idea that everything Desmond experienced in both his time travels actually happened. Here Eloise must have been going off information Desmond told Faraday off screen and then put in his journal. She knew everything that was going to happen that day exactly. There's no way Desmond could have changed the past, just like it was impossible to change the Incident.
The Constant- This also must have actually happened this way to begin with because Faraday put this stuff in his journal. Now after this happened Desmond was placed in jail for going AWOL, and Penny started writing to him, wanting him back. She finally gave up and became engaged.
2000
The Man From Tallahassee- It took a bit longer, but Charles ended up finding Locke too. He knows Locke will eventually find his way to the Island, and he wants an "in" with him when that happens.
2004
Walkabout- So Samuel sees Locke and, knowing he has a huge part to play in the future, lets him live.
Solitary- The first time we hear the whispers. The trapped souls might be warning Sayid that their really are others on the Island. They end up getting their point across in a round about way, but it still works.
Outlaws- The whispers again. Maybe the trapped souls were trying to help Sawyer learn how to hunt boar for the group, or maybe the boar really did have something to do with Sawyer's mark. This will just have to stay ambiguous, I guess.
Deus Ex Machina- So perhaps Locke's vision was meant to steer him away from opening the Hatch. I guess it was probably Samuel who prompted the dream. Although I'm not positive how this would fit in with Locke loosing his ability to walk. Perhaps Samuel did that too, to eventually get Boone killed.
Exodus, Part 3- This time Samuel sees Locke, but tries to pull him into the underground tunnels. Maybe he was trying to show Locke the tunnels so they wouldn't need to open the Hatch and would then have left him alone. Jack changed that plan though. The whispers were apparently trying to warn Danielle about the Others kidnapping Walt. Weather she sat the fire or they did for some unknown reason is still unclear to me.
Man of Science, Man of Faith- Water Walt? With whispers? That's weird. My theory is that Walt being in distress manifests his abilities by making the whispers personify themselves as him. So this is actually the trapped souls warning against getting involved with The Swan.
Abandoned- More Water Walt. More whispers. The trapped souls were obviously trying to warn Shannon about her impending death. Oddly enough if they hadn't freaked her out in the first place she would have never been out there to get shot.
The 23rd Psalm- Samuel searches Eko's soul to see if he will be on Jacob's side or his own. He finds him lacking that quality Jacob is looking for, and lets him live.
?- So the visions were from Jacob? Trying to get someone to keep pushing the button now that Ben had shaken Locke's faith in it.
Live Together, Die Alone, Part 1- The Hurley Bird. Well the epilogue explained that one.
Live Together, Die Alone, Part 2- The whispers here must have been the trapped souls trying to help the survivors be on guard just before the Others attacked them.
The Cost of Living- So now after all that Eko has gone through, Samuel must believe he will end up aiding Jacob's side, and not his. He takes Yemi's form to drive him a little crazy before killing him.
Operation Sleeper- Juliet implies that it was actually Ben who blew up the submarine, not Locke. Perhaps this explains why Locke came back from the sub soaking wet, when there was no reason for him to get in the water. Somehow he might have had second thoughts and Ben stole the dynamite from him at the last minute.
The Man Behind the Curtain- The cabin was once Jacob's home, but has since been taken over by Samuel. Ben knows it will be empty and is very surprised to find that Locke has an experience of Samuel there. Ben is unsure of exactly what has happened, but realizing Locke is more in tune with the Island than he will ever be, he decides to kill him.
Through the Looking Glass, Part 1- Since Ben has never seen Jacob, Richard must be the intermediary between them. At some point Jacob must have sent a message to Ben telling him two things. 1) That the Island was soon to be attacked by Widmore's people. To better hide the Island, Ben sent two of his people on a covert mission to block all radio transmissions from the Island from the moment the purple haze filled the sky. Ben must have known this was going to happen as well. Later to make sure no one could leave the Island and lead Widmore back to it, he destroyed the sub and blamed it on Locke. 2) That another plane would one day be coming to the Island, and that a runway needed to be build for it to safely land. As far as Walt goes, the only theory that satisfies me is that this wasn't Walt at all. Locke's subconscious wanted some reason to live, and gave himself a reason to embark on a new mission, reverting to his Island spirituality of old, believing it is the survivor's destiny to be here. But he can't bring himself to kill Jack to defend his belief.
The Other Woman- Though this episode is actually the one that lends the most credence to the defunct "The Others transport around the Island by the whispers" theory, the whispers in this episode must have been the trapped souls warning Juliet not to have anything to do with Ben any longer. Jacob's lists must have been the lists compiled by the Others, then later approved or changed by Jacob. The list was just for the people who were ready to join the Others at that point. Since the Candidates weren't ready yet, they weren't on Jacob's list.
The Shape of Things to Come- Ben uses his ability to call Samuel to attack the mercenaries. Where this summoning device comes from and what it is is the first totally unanswered question as far as I'm concerned.
There's No Place Like Home, Part 2- The trapped souls try to warn Kate and Sayid from helping rescue Ben. They know that their payment for this deed, leaving the Island, isn't their destiny.
There's No Place Like Home, Part 3- I believe the Christian who appears to Micheal just before his death really is Christian and not Samuel. The whispers imply he is one of the trapped souls on a mission for the Island.
2005
Because You Left- Daniel seems to have known what was going to happen after Ben moved the Island. The wheel must be very prone to coming off it's axis each time the Island is moved.
The Little Prince- Who the people in the other raft where is still a mystery. That makes two totally loose ends.
This Place is Death- Samuel must have turned Rousseau's team to his side. Samuel being in the well in the past must mean that he (and perhaps Jacob as well) traveled with the survivors during their time flashes. Samuel knew Locke and survivors would travel through time, and making the Island skip was his way of prompting that to happen. He wants the Oceanic Six to come back because he knows they have a part to play in the past. After the Island stops skipping he must have returned to his original time period.
The Shape of Things to Come- So Ben moved the Island before. Interesting. Maybe he did it after banishing Widmore so that he couldn't find his way back.
2007
Something Nice Back Home- Jack almost has a chance to talk to his dad the way Hurley talks to Charlie, but he misses it.
The Incident, Part 1- Ilana was hurt in a conflict with Widmore's people. But Jacob needs her to get back on the job immediately.
The Life and Death of Jeremy Bentham- Widmore was visited by Jacob, who converted Widmore to his side. Jacob told Widmore that Locke had to help return the Oceanic 6 to the Island. He also let him in on everything going on with the Man in Black and his future plans.
Because You Left- The fact that Desmond remembers his encounter with Daniel at this point just must be part of Jacob's plan. Otherwise you'd have thought he would remember it as it is happening back in 2005.
316- The entire requirement of Jack giving something of his father's to Locke must have been simply Eloise and Ben's way of inching Jack farther towards becoming a man of faith, versus a man of science. Eloise knows he will eventually end up embracing something he has no hard proof for.
Dead is Dead- Ben wanting to be judged by Samuel for returning to the Island is odd. Why he wants to do this is the third lingering question I've come across. Samuel must not loose his ability to change appearances until after Jacob dies.
LAX, Part 2- The waters in the Temple are how Ben was healed in 1977. They caused him to be "baptized" into Jacob's cause. When Jacob dies the waters become infected with the power of Samuel instead. Not knowing if the healing would work, the Others think Sayid is dead. Miles knows he didn't die but is confused as to what is happening. When Sayid wakes he is infected with Samuel's "spirit."
What Kate Does- The test that Sayid undergoes is being covered with Jacob's protective dust. If Sayid had been healed by the water under Jacob's power, the dust would have protected him from the torture. Since he was healed by the power of Samuel, the dust had no effect.
The End, Part 2- Although it's probably just poetic license so that the show can end the same way it began, how Jack got out of the cave is the final unexplained mystery of the show.
Timeless Purgatory
Lighthouse- I think David is actually Christian. Taking the form of Jack's son was an even better way to let Jack work through his issues than having another chance with his father would have been.