As a medical writer specializing in infectious disease, I can tell you that I whole-heartily support their appropriate use. There are a few that I have doubts as to the real necessity, such as the varicella vaccine for children (although it is a valuable and important vaccine for those over 65), but for the most part, not about safety and efficacy.
I do not trust most internet sites, even those run by doctors, unless they carry the HONcode label, indicating that they abide by the principles of the
Health On the Net Foundation. This is a red box enclosing the red and blue HONcode logo and is usually found at the bottom of the website page. This foundation was established to combat information passed off as medical advice by charlatans and by companies whose only purpose is to sell you something that is usually medically unproven.
Many would say that the "evil" big pharma companies should be included in the latter category, that they're only in business to make money. There is some truth to this, to the extent that, like any company, they need to finance their research to make safe products and, of course, be profitable. No company can survive as a nonprofit. You should know, however, that most pharmaceuticals, vaccines included, can cost millions of dollars to develop. Those development costs include extensive clinical trials conducted in multiple phases, culminating in very large based, typically international trials (to encompass a wide breadth of populations with different physiological characteristics) involving careful administration and observation of tens of thousands of individuals. (I am not employed by, nor to I write for, any pharmaceutical companies.)
In contrast, most of the "alternative" positions you'll find on vaccination are based on anecdotal situations, often involving only a few people. You can't draw good scientifically sound conclusions this way. Good science requires very carefully controlled experimentation and large numbers "subjects" for accurate statistics to be gathered and appropriately interpreted. Generally, experimentation is blinded or double-blinded, so that it is not biased by expectations what the experimenters hope to prove or see. Most scientists I know are of the highest integrity, who insist upon exacting and careful procedure -- both because they value their results and reputations, are generally humanitarian at heart, and because there are very, very strict government guidelines imposed by the FDA, and usually by the hospitals and medical centers involved in the testing process. Very often, external independent clinical research management companies oversee large scale studies. Yes, there are certainly unethical scientists out there, eager to make a buck by promoting their own ideas, or so stressed over the need to "publish or perish" the research gets rushed or falsified. Eventually, the scientific peer-review process catches up with and discredits them, usually because the work cannot be reproduced by anyone else. Unfortunately, some of these individuals can do a great deal of damage before that happens.
In contrast to this, most parties that I've read opposing vaccination have some kind of alternative agenda they are supporting. Some are simply fearful of science that they can't or won't understand. Many draw indirect conclusions from half-truths and outright lies.
In my opinion, the best unbiased information can be found in the medical literature, which can be accessed by anyone at PubMed.com. This is the website of the national medical library on the NIH (National Institutes of Health). The database is searchable using easy, logical terms. As an example, if you enter in "vaccination," a long list of possible associated topics will be displayed. If you want to search on multiple terms, use AND, OR, and NOT to connect terms (all caps). For example, entering in "vaccination AND controversy" currently calls up 215 articles. Most articles will have free abstracts that give an overview of the entire paper. Some articles are open access and can be downloaded for free. Unfortunately, publishers need to protect their copyright and support their businesses, too, so most articles are now available on a pay for download basis, which can cost anywhere from $10 - $60/article. If you go to a large university library, such as the UCLA biomedical library, however, you can usually access most articles for free, although you'll have to pay for copying if you want to take materials with you. Of course, it does help to have some background in science or medicine though, although the more you read, the better you'll get at following scientific design and interpretation. Journal editors are requiring more and more transparency; authors are required to list their affiliations, and are now more often asked to also acknowledged in the article external writing and financial support.
What I keep in mind is this. Before we had vaccinations, thousands to millions of children and adults died each year from diseases that we can now prevent. When is the last time you heard about a case of smallpox (presumptively eradicated in 1979)? This disease killed between 300 and 500 million people in the 20th century alone. Now? No one. Parents no longer have to worry about losing children to killers such as diptheria and polio. Parents in the third world praise organizations such as the Bill and Melinda Gates foundation, which provides free vaccinations for many diseases in poverty-stricken, medically-sparse areas. Birth rates in many of these areas are declining, as parents worry less about having large families to ensure the survival of a fraction of their children, and many countries are making large forward economic strides because of this. Frankly, I think the millions speak far louder and more convincingly than the relatively small population of nay sayers.