Yeah he is Dharma. Look at a the Dharma brain washing video. In it you see lots of Dharma things. Plus on season 3 DVD it is Labeled "Dharma Brainwashing Video"

In the video it says "God loves you like he Loved Jacob"

This means Dharma knows about Jacob. So either they Loved means he used to be Dharma but turned. Or he is still Dharma and the Loved means past love and current love. Or maybe Jacob died or faked his death? Maybe Dharma Experiments are to blame for the reason Locke couldn't see him at first. Why did he say "Help Me". Maybe He is held hostage by the Cerberus or the Others. What are his lists for? What do they mean? Why didn't Ben here what Jacob said to Locke? Can Jacob speak in peoples heads? Does he have a power were he can make people not see him and people not here him sometimes. One reason he may have said Help Me was because he knew it would be something Locke would pay atiention to. Ben shoots Locke because he heard Jacob. So if Locke didn't here Jacob he wouldn't have been shot and wouldn't be able to see "Walt" and Kill Naomi. Maybe Jacob can see the future? Another reason why his lists would be important. Did Jacob figure out how to change the core equation of the numbers? Maybe thats why the others are listening to him. Maybe thats why they take whatever there doing so serious.

This fact that Dharma new about Jacob and that they loved him at a time opens up tons of theories.

If you want you can think up some more theories or post what you think about mine.