Are there any high profile cases of conflict of interest in research?
The manipulation of research and press coverage by the tobacco industry on the health effects of smoking would make an excellent case study (see e.g. Bero, 2005), not least as many leaked internal documents have come to light over the years which leave no doubt as to this having been a deliberate policy.


  One infamous internal memo from the Brown &amp; Williamson tobacco
  company, typed up in the summer of 1969, sets out the thinking very
  clearly: “Doubt is our product.” Why? Because doubt “is the best means
  of competing with the ‘body of fact’ that exists in the mind of the
  general public. It is also the means of establishing a controversy.”


-- The problem with facts, Tim Harford

Just one example would be the attempt to refute an influential Japanese study on the effects of passive smoking. The actual employees of the industry were left off the study to confer some distance ("ghost authors")


  The tobacco industry generated a study, the “Japanese spousal study,”
  in an attempt to refute the findings of a 1981 cohort study showing an
  association between secondhand exposure to tobacco smoke and lung
  cancer 
  
  The parties involved in conducting the study
  included a tobacco industry scientist, a tobacco industry consultant,
  an industry law firm, and two Japanese investigators. The consultant
  was the sole author of the final publication 


-- Hong and Bero (2002)

Interestingly, the picture is not completely negative, as Big Tobacco's policy of "distraction research" (funding unrelated research for good PR) led to some important high profile discoveries and Nobel Prizes.


  Prusiner is a neurologist. In 1972, he was a young researcher who’d
  just encountered a patient suffering from Creutzfeldt-Jakob disease.
  It was a dreadful degenerative condition then thought to be caused by
  a slow-acting virus. After many years of study, Prusiner concluded
  that the disease was caused instead, unprecedentedly, by a kind of
  rogue protein. The idea seemed absurd to most experts at the time, and
  Prusiner’s career began to founder. Promotions and research grants
  dried up. But Prusiner received a source of private-sector funding
  that enabled him to continue his work. He was eventually vindicated in
  the most spectacular way possible: with a Nobel Prize in Medicine in
  1997. In his autobiographical essay on the Nobel Prize website, Prusiner thanked his private-sector benefactors for their “crucial”
  support: RJ Reynolds, maker of Camel cigarettes.


-- The problem with facts, Tim Harford

Bero L. A. (2005) Tobacco industry manipulation of research. Public Health Reports. 120(2):200-208.

Hong, M.-K., &amp; Bero, L. A. (2002). How the tobacco industry responded to an influential study of the health effects of secondhand smoke. BMJ : British Medical Journal, 325(7377), 1413–1416.