Here is a good and balanced view of the controversy over mercury, vaccines and autism. Personally, I agree with his view in general. Also, his view as a research neuroscientist that even small amounts of toxins can cause the brain to not function well is right on.
Another thing I think important is to spread out the vaccination schedule for the child. We used to vaccinate on a much slower schedule. The rise in autism appears to coincide with an acceleration in that schedule beginning around 1991. Challenging a childs immune system with so many vaccinations when their immune system (and most other systems) are not yet fully developed does not seem wise. Here is a more user friendly recommended schedule from a doctor Miller.