With articles by the New York Times, CNN, and RF Kennedy Jr. , people keep asking whether autism is triggered by vaccines with mercury-based thimerosal. Here's a partial reading of the debate from a Jewish standpoint.
The debate about vaccines and autism requires us to judge correlations. For instance, does the onset of autism correlate to thimerosal vaccinations? More importantly, does the incidence of autism rise and fall with the level of mercury-based vaccinations in a population? Maybe there's data to support these correlations.
But are these spurious correlations between thimerosal and autism? Unfortunately, the question of spurious correlation is tough to answer. We lack adequate biochemical (etc.) knowledge of how mercury effects the spectrum of autism(s).  It’s also difficult to identify and eliminate other triggers (besides vaccines) of autism(s). Furthermore, epidemiological correlations are hard to substantiate because we are not running a controlled experiment on human children.
Instead, critics might say we are running a massive uncontrolled experiment with thimerosal. Keep in mind, though, that there is an enormous health benefit associated with vaccines. Fortunately, thimerosal has been eliminated from some vaccines. Yet, policymakers are continuing with the virtual experiment with mercury-tinged vaccines because these are still the best vaccines for the flu. (And influenza is a serious health threat, as you can see by checking the spanking new wiki flu website set up by Effect Measure and friends.)
Turning now to my Talmudic daf yomi readings. To a modern reader, the rabbis are dealing with a problem of correlation: do amulets protect the health of animals? (bShab 53b) If amulets truly correlate with health, then they may be carried on Shabbat. If amulets do not work (= if amulets and health are a spurious correlation), then carrying them is a form of prohibited sabbatical work.
Lacking biochemical (etc.) knowledge of sickness, the rabbis judged the efficacy of amulets by two critera (bShab 61): medical efficacy and expertise. First, amulets are deemed effective if they cure or prevent sickness three times (3x); Second, healers are deemed experts if their amulets cure three times (3x). Wisely, the rabbis did not assume that amulets that cured humans would necessarily work with animals. 
By these Talmudic criteria, one might be inclined to approve thimerosal vaccines. Vaccines prevent diseases at a high rate. Conversely, there are scanty correlations to argue that thimerosal vaccines cause autism. Furthermore, the scientists who proclaim that thimerosal is linked to autism are vastly outweighed (in number and reputation) those scientists who question the alleged link to autism. (see, e.g., Autism Diva on Geiers, Orac on Kirby) Looking at the quality of experts and the data, one might expect Jewish law (halakhah) to favor the use of thimerosal vaccines.
However, these Talmudic criteria may not be sufficient. After all, Jewish law here judges amulets only in terms of Shabbat. The downside to poor judgment on an amulet was small. With a mercury-based vaccine, the downside to poor judgment might be an increased incidence (but not an epidemic) of autism. Or unvaccinated exposure to disease. Furthermore, there is the hermercurial factor: Kennedy is right that the pharmaceutical industry is investing well in Bill Frist and other politicians. It would be best if we could avoid the thimerosal choice altogether.
Therefore, with so much at stake, there are forceful reasons to find/fund alternative vaccines and public health measures to tackle flu and the remaining diseases now fought with mercury-derived vaccines. Plus, the precautionary reduction in U.S. and Eurpoean thimerosal use should be applied to Third World countries, too. Meanwhile, in Jewish communities, let's think about vaccination decisions by parents and the needs of autistic children (cp. programs in Balitmore MD and Newton, Mass.). Kol tuv,
 Excepting, e.g., Deth study cited by Dwight Meredith
 Starting with the gemara at bShab 61a-b, Talmudists apply the 3x criteria with permutations involving 3 different amulets, diseases, patients, or healers. Unwisely, some drugs have been marketed to humans based merely on animal testing results. Prime example: thalidomide.