I think the storyofstuff film raises some very good points and real problems with cap and trade as it currently stands, but i think that emissions trading can play a role and have a positive impact, because it can motivate significant activity in the right direction - but to do so it has to be properly constructed and regulated to avoid some of the issues the film raises...
However, that said I also think this film is very accurate on carbon offsetting at a personal level: http://www.cheatneutral.com/