go out and buy the 'vaccine book' by robert sears. (i don't get any kick-backs, i promise). he goes through each vaccine in detail, the pros and cons and the evidence behind any issues. the nice thing is he doesn;t tell you what to do, he just lays out all the info for you to decide.
the thimerisol/mercury issue is really a non-issue since several studies have disproven that association, and for many years now, most of the vaccines have not contained it.. the only one that still does in the multi-dose flu vaccine and your kid can get the single dose-thimerisol free one. the other is the multi-dose tetanus, but that is just the booster shot for adults, not the one the kids get.
the other controversy is whether the 'inflammatory response' triggered by vaccines actually sets off a course of events leading the kid to have autism.
autism is extremely complicated and i don't think 'vaccines cause autism' but who knows if in someone who is genetically predisposed to have this disease, whether an environmental trigger (such as a vaccine, or even a bad naturally occurring illness) can set it off, make it occur earlier, or make it worse than it would have been otherwise.
the jury is still out.
now i am a physician and a toxicologist and i am vaccinating my kids, but i am doing it on a modified schedule...stretching things out a bit. the kids will still be fully vaccinated, and with the most important things first, but like the first response we are waiting a bit on the mmr. you can also split up the mmr and get each one separately. some people advocate this anyway, irrespective of the autism debate, since it is thought that you develop better, longer lasting immunity when the body only has to deal with one thing at a time.
get dr sears' book, i think it will help you understand alot.