Do funding sources necessarily affect the outcome of research?

Funding for scientific research has been drying up lately, and as a result I have been noticing more research tapping into unconventional funding sources.

A recent paper in the highly-respected journal Nature showed that barefoot running generates smaller collision forces than running in supportive shoes. This study was funded in part by Vibram USA, a company that produces minimalist shoes to simulate barefoot running.

A group of organizations committed to showing that vaccines cause autism recently promised to fund research “replicating” the work of a specific scientist responsible for the hypothesis that vaccines and autism are related.

So on the one hand, this kind of funding seems to make a priori assumptions about what the outcome of the study will be and runs the risk of biasing the outcome. But on the other, if the methodology is sound, does it matter where the money came from?

In a world where government money is drying up, companies with a vested interest in the outcome of a given research project may be the best bet to get your research funded. It is in the best interest of both the company and the scientists to work together. So do you trust research with a monetary conflict of interest? Why or why not?