Jacob is causing the dreams, and MIB is causing the visions
When you look at the result of any given dream, it appears that they would benefit Jacob. The messages also resemble Jacob (guidance, further instructions, helping people follow their faith).
It seems that MIB can physically influence people, while Jacob may only be able to appear to people in dreams. This goes back to fate vs. free will/science vs. faith. When Jacob appears to people in dreams, he is not physically forcing them to do anything. He just puts the idea in their head, but it is ultimately up to the individual to act on the dream. If you look back on the dreams, they were usually to guide people, to help them get where they needed to be.
The visions physically led people to bad things. The first vision ever was Jack's Dad, and he led Jack off of a cliff and he may have died had Locke not been there. (Walt led Shannon to her death, and Yemi (MIB) led Eko to his death). But if you look at Eko's initial dream with Yemi, Eko was trying to apologize to Yemi for contributing to his death, but Yemi said not to worry and told him of the importance of pushing the button. But when MIB used Yemi to try to get Eko to confess, "Yemi" was very scornful and did not act like he did in the dream. And right after Yemi and turned into the monster and killed Eko.
This is also science vs. faith in the sense that when Jacob sends someone a message in their dreams, the person must have a lot of faith to follow that message. When MIB appears to someone physically right in front of them, you assume that is the right thing to follow since it is right in front of your eyes. True faith is following what you believe even when what you are seeing in front of you tells you to do otherwise.
MIB/Monster is causing the dreams and visions
Most, if not all, these dreams and visions are caused by the Monster.
The Island is a waypoint for the dead. For visions of the dead, there is a distinction drawn between visions of people who died off-Island and dreams of those who died on the Island. Those who died in reality, off-Island (such as Christian Shephard, Ben's mother, and Yemi) re-appear on the island to otherwise conscious and lucid characters. They interact with the characters and seem to be a part of reality and the environment. Conversely, those who died on the Island appear only in dreams (such as Ana Lucia's visitation to Eko in his sleep) or drug-induced hallucinations (Boone's role in Locke's vision quest)--they do not "re-appear." Those who "die" on the Island move on to their final destination, assisted by The Monster.
When Locke's father appears, he claims that he died right before he appeared on the Island. His interaction with Locke is consistent with the other visions of the dead, in that he appears to be living again on the Island.
Aaron has a stong connection to the Island via dreams. When Sawyer asked Kate if she was sleeping well over at Claire's with the baby being there, Kate responds saying that Aaron's a good sleeper. (minor interaction)
Jack and Hurley are the only ones of the O6 who are seeing these visions because they are the only two of the O6 who were on Jacob's list. The Island/Jacob is trying to communicate with them in this way.
The characters who are appearing (Charlie and Christian) are not dead, they are "undead." Undead in the mythology of LOST is someone has been on the Island and has died, but we see them in a different time-line. A number of our favorite characters on the Island are really "undead," having died during their stay on the Island. And this would include Christian, since I think he has been on the Island in the past and has something to do with DHARMA/Hanso/Widmore etc.
In Support: The mercenaries from the freighter made a point of burying Danielle and Carl. Weird considering there are a number of ways they could hide the bodies from discovery than spending time digging a hole - why not just throw them off the path? It could be argued that they were worried about losing their element of surprise before attacking the village, but it seemed to me they attacked the village almost immediately with the bodies behind them. Also Locke once said "nothing on this Island stays buried".
Against: Both Libby and Boone have appeared in apparitions after both were buried. Libby this season, to Michael, on the boat. Boone also showed up in Locke's vision when he was in the sweat lodge.
The producers stated Boone's appearance then was simply part of Locke's dream. See the March 21, 2008 podcast.
These apparitions aren't visions, they are entirely real. The Island is the gates of the underworld. Cerberus, the smoke monster, is the protector of the underworld. It is not heaven and hell, like in modern religion. But just one place, where all the dead go, no matter what kind of life they led, as in old mythologies. Charles (and possibly Alpert) are some kind of "gods" that live forever, and are battling mortals (Ben) for control of the Island. The whispers, the visions, etc..., are all real, only some people have the ability to see and hear the other side.
There is no evidence to support that only certain people can hear the whispers. Whenever the whispers are heard, its pretty clear that everyone involved can hear them.
Most of the dead people who have appeared on the Island have appeared in dreams. The only two I can recall who have appeared in 'real life' are Christian Shephard and Yemi, both of whose bodies are missing: Christian's wasn't in his coffin and has never been found, Yemi's vanished from the plane after it was burnt.
The Island is only reaching out to those who left the Island and are not doing what they can to protect it. Michael, Hurley, and Jack all left and attempted to return to their original lives, hence why those three all receive regular visions from "the Island." Sayid is obviously doing his part by working for Ben, Sun is presumably planning to do something by taking over Paik Industries, and Kate is doing something for Sawyer. Aaron is probably also doing everything he can as well.
This theory makes no sense at all. Sayid is working for Ben, but who knows if Ben knows what is truly best for the Island (he killed Jacob the first time he me him). Sun doesn't seem to care about the Island, she just wants to find Jin again. Kate isn't doing anything for Sawyer or the Island, she came back to find Claire because she felt guilty about taking the baby and lying to everyone about it while Claire is nowhere to be found. "Aaron is probably also doing everything he can as well"... Aaron is 3 years old. I doubt he is doing any more than any other 3 year old would be.
The apparitions are the consciousnesses of those who exist in the alternate timeline, but were killed in the original timeline. They still exist in some non-corporeal form because their counterparts are alive and well in the alternate timeline. It's interesting to note that (with the exception of Boone and Charlie) all the survivors of Flight 815 that were killed in the original timeline were not shown to be present on Flight 815 in the alternate timeline (Ana Lucia, Eko, Libby, Shannon, Michael, Artz, Nikki, Paulo). It could be that the two timelines will merge at some point, and that everyone's consciousness will merge as well.
The "ghosts" are basically manifestations of the electromagnetic energy with variable degrees of being "real", and can be given form by all kinds of different "sources". Similar to the beings that we see in the after-life/FST.
The ghosts and whispers are the result of alternate realities bleeding into the "main" reality.
...refers to both Jack and Kate. As Richard Malkin initially suggested, Claire is supposed to raise Aaron herself. This is part of the reason that Jack comes to believe that they were not supposed to leave the Island, and must go back.
Malkin was lying when he confessed, that was pretty obvious. Malkin wanted Claire to raise Aaron, and he bugged her for months. Then he sent her on Flight 815, he did that because he knew that she would end up on the Island and she would HAVE to raise him. Malkin's daughter told Eko about talking to Yemi when she was "between places" after she drowned. No way she could have known about that.
...refers to Christian, Jack's father. Jack is not supposed to raise his father from the dead. Hurley only asks if he thinks this is about Aaron.
...And appears to be in a literal "time loop," busy knocking the same tree over and over again. Time travel, plot point, and Greek mythology parallels rolled into one visual burrito! (At this point, there's not enough information to form a theory, as our equation is covered with way too many variables (especially this being a dreamlike vision and all), but the show has proven time and time again that no element is too small).
People, including the dead, appear to "the chosen one" in dreams and give them the direction they need to lead their people and to protect the Island. This is why Ben said, "I used to have dreams, too." Ben used to be lead by his dreams the way Locke is now experiencing it. Either Jacob or "The Island" are controlling these images that "the chosen one" sees.