From what I understand, Khan keeps the videos unscripted so he can maintain more of a conversational style, but he's always careful to understand the material very well before doing a video on a subject.
One thing I found quite frustrating was the lack of technology applied to making the video - in the few I've seen he takes ages drawing out number lines (for example) and the writing is quite unclear; it doesn't appear to be too hard to have a marked axis that you can paste in when it's needed. Petty issue but something I didn't expect to find on this much touted resource. Another example would be hand drawing bunches of marbles/tins http://www.youtube.com/watch?feature=player_embedded&v=D...; I guess it naturally limits the pace, which may be good.