After our discussions here and others I've had on other sites, I think there are three main candidates for Jacob's ghost. I'm currently revising some existing theories and working on another that's new, so I'm curious which scenario you all find the most plausible. Keep in mind that the theories linked were both posted BEFORE recent events and thus wrong on a lot of details. That said, feel free to offer any general suggestions for revision and improvement.
1) Jacob is the ghost of Magnus Hanso. Ben's special ability is to channel the Mind of Magnus...
2) Jacob is Alvar Hanso, whom Ben has imprisoned in some ghost-like state.
3) Jacob and Alvar are brothers and the descendants of Magnus Hanso. Alvar eventually left the Island but Jacob remained behind. Eventually, Alvar returned and established the Dharma Initiative to determine whether humanity could co-exist with special people like them, who are destined to take humanity's place as the dominant species on this planet. Jacob was killed in the Incident and now longs to wipe out humanity to preserve His people.
So what do you think? Which of these general explanations do you prefer? My current favorite is some combination of one and three, but I'd love to hear your thoughts!