I don't want to stir up an argument over what actually "was" in the briefcase in
Pulp Fiction mainly for the following reasons:
The case is, as Sylvar and others have pointed out, a MacGuffin (see http://www.straightdope.com/mailbag/mpulpfiction.html), and has no bearing on the plot,
There is no way to deduce its contents with any degree of certainty from what is presented to the viewer, and
Tarantino has already revealed that, during production, a standard alkaline battery and a lightbulb were used, as Ninja-Lad reveals.
I would, however, have no hesitation in throwing out another theory just for the diehard Pulp Fiction fans like myself who always love a new spin on the plot. Mine is slightly less melodramatic than the "Marcellus' Soul" or "Resevoir Dogs' Diamonds" theories which are so popular, and has slightly more evidence than the equally cool "Repo Man Alien's Body" theory, which is unsubstantiable.
So here is my theory of what is inside the case: an Academy Award
What leads me to think so? Anyone who has seen "Swimming With Sharks" will know that Frank Whaley, who plays the unfortunate chap eating a Big Kahuna Burger in Pulp Fiction, played the part of an assitant to a big-time Hollywood executive in that movie. Marcellus Wallace's wife was a failed actress, so is it inconcievable that he found and hired someone in a position to steal the most coveted acting trophy in the world, to give to his wife as the biggest pick-me-up present ever? While this would take some creative cross-film referrencing by Tarantino, this is a very satisfying possibility to me. I would chalk up the "666" combination to that number being one of the easiest for drug-dealing assasins to remember, rather than some mystical sign of a covenant with the devil. And to those who would question the golden luminence of a trophy, Oscars are coated in gold leaf.
Just some food for thought.