Right, before I begin I would like to point out - only read this if you have watched all three seasons because there will be spoiler material in this post.
I believe that the boat coming is probably an old group of people from the island, hence they seem to know of it's existence and roughly where it is. Possibly people who survived the purging from Ben's flashback and are coming back on their own terms to attempt to take over the island. Because I would guess that Ben seems to know who they are judging from the way he reacted and the genuine worry he showed. The people on the boat also seem to have a good idea that the Oceanic Flight 815 crashed their, although they weren't sure, I get the feeling Naomi may have made the death thing up on the spot or had been told to use that story to mentally mess up the losties.
The island itself I believe to be not far from what we know already, an island bought by the Hanso Foundation for scientific study. Possibly bought outside of USA jurisdiction so they didn't have to adhere to the laws as I fully imagine brainwashing and other mental tests are performed. I believe however that it was mainly animals tested - the purge may even have been when people disagreed to human testing.
As for the people - I believe Ben has compromised Locke, but also now got very worried as Locke seems to have more respect from the others and may take the head of the others command as it were. Jack and Kate obviously get off the island and I can only imagine however in the way that the ending of S3 was portrayed that people were left there with Jack's conscience meaning that he would beat himself up mentally knowing they were there unable to escape.
As for the next season, I am predicting a fairly island orientated storyline, going back to the history of the island, which fits in with my ship theory as well as it wouldn't be a huge leap to get to some of the characters in a flashback of Ben/Juliet.