While doing some research into open access journals, I found this one at Public Library of Science:
The Chilling Effect: How Do Researchers React to Controversy?
The authors conducted interviews and surveys with researchers whose work had been exposed to controversy, mainly by accusations of wasted money. The findings:
The NIH defended each grant and no funding was rescinded. Nevertheless, this study finds that many of the scientists whose grants were criticized now engage in self-censorship. About half of the sample said that they now remove potentially controversial words from their grant and a quarter reported eliminating entire topics from their research agendas. Four researchers reportedly chose to move into more secure positions entirely, either outside academia or in jobs that guaranteed salaries. About 10% of the group reported that this controversy strengthened their commitment to complete their research and disseminate it widely.
As some others* have noted, all of the examples of "wasteful earmarks" that John McCain and Sarah Palin trotted out during the election campaign were appropriations for basic science or science education. It's bad enough that this encourages voters and lawmakers to think of these fields as wasteful; add to that the possibility that the researchers themselves will begin to shy away from their work and you get a double hit on science.
* At Dispatches from the Culture Wars, Panda's Thumb, or Pharyngula, can't really recall where just now. Doesn't matter - you should be reading them all, anyway.