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Now that we know that at least some of the apparitions on the Island are the work of Jacob's nemesis (and it's not unreasonable to assume that Jacob is capable of doing the same), I wonder whether a discussion of all the ghostly appearances on the island is in order. I've taken the list from the Lostpedia page and put down who I think is providing the apparition and why:
- Jack repeatedly sees his deceased father in the jungle. ("White Rabbit") MIB initially testing Jack's sorrow over his father's death to see if he is manipulable.
- Claire has a dream about looking for her baby, encountering Locke, and finding a crib filled with blood. ("Raised by Another") Don't know at this point, might just be Claire's stress affecting her dreams.
- Boone has visions of Shannon being killed by The Monster in the jungle, after Locke drugged him. ("Hearts and Minds") Again, Boone's worries over his sister - largely due to the hallucinogenic mix Locke cooked him up.
- Locke has a dream in which he sees the Nigerian drug plane crash into the Island and his mother pointing skyward. He becomes wheelchair-bound again, and also sees Boone covered in blood repeating the phrase, "Theresa falls up the stairs, Theresa falls down the stairs." ("Deus Ex Machina") MIB giving Locke his initial test. After Locke's miraculous healing, which is just down to the Island and no-one in particular, MIB wants to see if Locke is willing to do whatever it takes for him, even if it means somebody else dying. Locke passes this test...
Season 2 ("Everybody Hates Hugo")
- Shannon has three visions of Walt:
- While searching for Vincent. During this vision Walt says backwards, "Don't push the button. Button bad." ("Man of Science, Man of Faith")
- In her tent. During this vision Walt says backwards, "They're coming, and they're close." ("Abandoned")
- While searching for Walt with Sayid. Sayid also sees him in this instance. ("Abandoned")
These visions, I believe, are not intended to manipulate Shannon, but Sayid, who would react with extreme anger at the death of his lover. When Sayid is faced with Ana-Lucia and she gives him her gun, is when Sayid is tested for suitability to do MIB's bidding, and he fails.
- Hurley has a dream in which he gorges on food, speaks in Korean to Jin, and sees the mascot for Mr. Cluck's. ("Everybody Hates Hugo") This I put down to guilt on Hurley's behalf about his past.
- Kate sees a horse in the jungle that looks just like the one that allowed her to escape from Edward Mars. ("What Kate Did") Frankly I have no idea, this has always seemed quite random.
- Mr. Eko sees flashes from his past when confronting The Monster. ("The 23rd Psalm") An instance of The Monster 'downloading' information about Eko to use in the future against him, in order to manipulate him.
- Charlie has two dreams about needing to save Aaron, which include images of his childhood and a painting by Verrocchio. ("Fire + Water") Don't know.
- Hurley has visions of his imaginary friend Dave. ("Dave") Dave is MIB. If he could convince Hurley that the Island and everything else was not real, then he would do as he said, and if he later convinced him to kill himself, then his do-gooding influence on the island, as well as many people's faith in him, would be lost. Hurley failed this test.
- Mr. Eko has a dream featuring Ana Lucia and Yemi in which they tell him to help Locke, and in which Yemi instructs him to look for the "?". ("?") Knowing that Locke has lost his way and is in danger of not following his orders, MIB sends Eko to help him by manipulating his feelings about his past (info obtained in an earlier episode).
- Locke has a dream where from Eko's point of view, he climbs a cliff and meets Yemi. ("?") This IMO is MIB reminding Locke how special the Island is, and that even if Locke is not getting all the 'special' instructions, somebody is, and he should be willing to help for the good of the Island.
- Locke undergoes a vision quest in which he is guided by Boone and instructed to save Eko. ("Further Instructions") In contrast to Eko being recruited to help Locke, Locke is now being sent to help Eko, and MIB has the perfect thing to blackmail him with - the guilt of not pushing the button.
- Desmond has a series of flashes, in which he perceives possible instances of future eventualities:
- Locke giving a speech, saying he would go after Jack, Kate, and Sawyer. ("Further Instructions")
- Lightning striking Claire's roof, killing Charlie. ("Every Man for Himself")
- Charlie drowning trying to save Claire. ("Flashes Before Your Eyes")
- Charlie dying in the ocean from being slammed against rocks, while trying to catch a seagull for Claire. ("Par Avion")
- Desmond, Charlie, Hurley, and Jin trekking through the jungle; Charlie is killed by an arrow trap, and they find a parachutist. ("Catch-22")
- Charlie drowning while flipping a switch in a hatch; Claire and Aaron leaving the Island in a helicopter. ("Greatest Hits")
I think all these are not to do with Jacob and MIB, but part of the more general Island mythology, to do with electromagnetism and time etc.
- Mr. Eko has a confrontation with what he thinks is Yemi. ("The Cost of Living") Eko's final test - if MIB can get him to repent his sins, then he will have something to manipulate him with. Eko is unrepentant; so MIB cannot use him, and in a moment of anger, sends the Monster/becomes the Monster to kill him.
- A young Ben sees his dead mother on the Island. ("The Man Behind the Curtain") Aware of Ben's sad family situation, MIB uses Ben's love of his mother to try and catch him early, and succeeds eventually in recruiting him.
- Locke, in the mass grave site, receives instructions from what appears to be a vision of Walt, telling him he has "work to do". ("Through the Looking Glass") MIB rescuing Locke for future purposes (if he's dead he can't go on and do MIB's work now, can he?)
 Season 4
- Hurley has several visions of Charlie: once in a convenience store, in the LAPD interrogation room, and outdoors at the mental institution. On the Island, he also sees Jacob's cabin, which appears to follow him, then disappears after he wills it to disappear, much as he willed Charlie to disappear at the mental hospital. ("The Beginning of the End") The first apparition of Jacob in the show, trying to get Hurley to return to the Island, to bring his positive influence.
- Michael had two separate visions of Libby: once while in the hospital, and once just before he was about to detonate a bomb on The Kahana. Both of these appearances are connected to his guilt over killing her. ("Meet Kevin Johnson") Not Jacob nor MIB - as the list says, guilt.
- Off the Island Jack sees visions of his father while inside his medical office. He seems to only be seen by Jack. ("Something Nice Back Home") More Jacob trying to get Jack back to the Island by showing Jack his father and reminding him of the place where he last saw his father.
- Claire on the Island seems to be able to talk to her father, Christian. He seems to be able to pick up Aaron, so we know that her visions must be somewhat true. ("Something Nice Back Home") Don't know.
- Locke has a dream in which Horace Goodspeed is building a cabin for himself and his wife. He then tells Locke that in order to find Jacob he must find Horace, who has been dead for 12 years. ("Cabin Fever") MIB giving Locke the key instructions on moving the Island that will culminate in Locke's last travels through time, reminding him of his path and reaffirming his faith, so that he can die and return to the Island as a body for MIB to inhabit.
- Kate has a dream with Claire telling her to not take Aaron back to the Island. ("There's No Place Like Home, Parts 2 & 3") MIB telling Kate not to return - his plan is being executed and we all know how much Kate likes to mess with plans/disobey orders.
- Michael sees Christian, who tells him that "[he] can go now". ("There's No Place Like Home, Parts 2 & 3") MIB - "I'm finished with you now, Michael"
 Season 5
- Hurley has a vision of Ana Lucia, Were she tells him he has "work to do". ("The Lie") Jacob getting Hurley to concentrate and eventually get back to the Island."
- Walt says he had a dream of Locke being on the Island, in a suit, surrounded by people who want to kill him. ("The Life and Death of Jeremy Bentham") Don't know.
So, not a definitive list I know, but I hope you can see a trend, and maybe it could start some discussion.