Tarentino has said that he would never reveal what is in the case, because he wanted viewers to decide for themselves, which gives creedence to the "McGuffin" idea.
I, however, subscribe to the "Marcellus Wallace's Soul" theory, which goes like this:
The men in the hotel room that Jules and Vincent kill made a deal with Marcellus for his soul (they would have been agents of the devil), and Marcellus initially agreed. His soul was taken out through the back of his neck, which is why we see a band-aid on Marcellus in the first scene he has with Bruce Willis. Marcellus either changes his mind about it, or else feels he has been cheated, so he sends out his two "Guardian Angels" to recover his soul. They find the briefcase (which has the combination "666"), but are nearly killed when a man hiding in the bathroom (Alexis Arquette, now on The Surreal Life) empties a six-shooter at them from point blank range. Miraculously, neither man is hit. Vincent thinks that this is just a freak occurrance, but Jules is convinced that it is the work of God. He retires from his life of crime immediately after delivering Marcellus' soul back to him. Vincent continues as a hitman, and is killed in his very next assignment. So maybe Jules was right?
Truthfully, Tarentino probably didn't intend ANY of this, but I like it so much, I tell it to everyone who will listen.