Most of my personal qualms with Chopra stem from philosophical and spiritual disagreements. Inimilist's link covers how he has been duplicitous in order to spread his message and increase his wealth. The following link is concerned mainly with how his messages intercede with the medical community:
http://www.quackwatch.com/04ConsumerEducation/chopra.html
This is a small sample of scientific protestations, indicative of a much larger field of pseudo-scientific debunking. For those more interested in such materials I'd recommend John Diamond's Snake Oil and Other Preoccupations, which goes into far more detail about a variety of alternative medicine techniques.
In a nutshell, there's a reason "alternative" medicine isn't mainstream: it lacks testability, or the repeated results that legitimize mainstream medicine. Protests occur in the form of anecdotal stories, which is just that...anecdotal, not statistical. Very few will deny the occasional benefit of relaxation techniques to aid in healing, which would seem to endorse practices such as meditation or acupuncture. But these consistently show no benefits beyond more traditional stress-reducing techniques such as massages or simple rest. A placebo. Not harmful, but nothing special either.
The danger comes with more invasion forms of alternative medicine. Various ointments, pills, supplements, cure-alls, and diets. Chopra's personal snake oil goes into this realm by possibly being dangerous in sufficient quantities.
The dissenting opinion at the bottom of the link is fairly standard. Some appeals to the evil of organized business and/or medicine (almosy unanimously unsupported), followed by an anecdote that they use as definitive proof to the contrary.