Conflicts of interest are not a "conspiracy theory." They are actually present in the majority of studies, and they do indeed affect research outcomes.
Outdated but still a great analysis:
I find it helpful to track down the CVs or other biographical information on a study's authors. If you want to cut straight to the chase, do a search on somebody's name along with the name of a drug company, (e.g. Offit, Merck). For example, here is a bio for Dr. William Schaffner, a Vanderbilt University vaccine researcher who is quoted in an ABC story as saying that states with exemptions need to "tighten up" and take away the right to informed consent:
Below is a link to the BMJs policy on declaring competing interests. This can be a useful guide on the types of competing interests that can affect research.
When pediatricians and public health officials whine to the media about us bad widda mommies using the Internet, they'd do well to know that this is the kind of stuff that we're reading.
Good luck with your research!