At first glance this documentary/fiction/cartoon is quite entertaining and thought provoking. Of course, when something provokes thought, it can then be scrutinized. The reality is this movie combines metaphysics with innuendo and baseless conclusions. The link that "What the Bleep..." would have you see between science and spirituality is, in fact, not rooted in science at all. The Transcendental Meditation study mentioned in the film claims that meditation by a group can reduce crime in a given area, Washington D.C. in this case. In reality the HRA (Homicides, Rapes, and Assaults) crime rate was about 30% higher in 1993 than the average crime rate between 19881992. There was absolutely no decrease in the homicide rate during the study. In fact, each and every claim that links metaphysics to science can and has been debunked.
My conclusion from this information is that this movie is either a poor attempt to indoctrinate people or a joke. Either way, I suggest that you do not waste your time.
If you are looking for a long winded movie about science that could provoke thoughts, you might consider Mindwalk (1990).