In Star Wars IV 'A New Hope', Obi Wan Kenobe disappears when he is killed. Also, in 'Return of the Jedi', Yoda disappears when he dies. Therefore, why does Qui-Gon Jinn not disappear in 'The Phantom Mennace'? Also, Darth Vader does not disappear when he dies? What's going on there?!
Both Yoda and Obi-Wan accepted death and were absorbed bodily into the force. In fact you see Obi-Wan stand there and wait for the blow that 'kills' him, as he knows it's time to move on ... Qui-Gonn is too big-headed too think it can happen to him, and Darth is too preoccupied with chucking emperors off cliffs ... Sound plausible?
I read on the Official Star Wars web site that Rick McCallum(Lucas's right-hand man) asked him this very question. Lucas (typically) did give a straight answer. This matter has not yet been resolved but he has gone on record saying that it should all become clear in Episode 3
The Jedi force is in them and they change into spirit form because they are fighting for the good stuff. However Vader doesn't dissappear because he is not good and is a sith.