I love how people say these things are rigged like it's some big secret. Obviously they are rigged with certain algorithms, anyone over the age of 8 should know that. Next thing you're going to tell me is that a slot machine is just based on your own personal timing. (However, like a slot machine these little buggers should be regulated.)
The other theory making the rounds that may have already been mentioned is the biblical story of Jacob and Esau. Kind of seems funny now since the story goes Esau gave up his birthright to Jacob for a bowl of soup and in the beginning of the season finale Jacob has asked the other guy if he wanted some fish to which he replied "no thanks I've already eaten."
Also notice when Jacob is referring to building the thread he is not looking at Locke who is inspecting the loom he's looking at Ben who is inspecting the column with the drawings.
Any thought that Jacob may have double-crossed his enemy and it wasn't him that was killed in the tomb under the temple and he somehow used a similar power to switch bodies? Another thought was the whole "thread building" Jacob was talking about was an elaborate plan to make sure he doesn't die. Which might be possible if the bomb the Losties set off makes enough changes to the future. This might even have even been predicted and drawn out on the column that Jacob's enemy inquired about when entering the tomb. I thought it depicted a sun at first but it might actually be the light from the bomb explosion.