This is a long and complicated topic, so I’ve hesitated to wade into it.  But since my default setting is to be wary of new and improved and highly touted health related products,  I never did buy into the craze for hand sanitizers.  I’ve found some good sources on this issue, some scientific and some in the mainstream press.  The main culprit seems to be triclosan, a biocide, that can have some nasty side effects on development if ingested.  Long story short, it hasn’t been regulated much yet, in spite of some real dangers related to its use (nosocomial infections, accidental ingestions in children, increased antibiotic resistant bacteria, increase in asthma in adult users to name a few.)
A study out of Madrid showed induced resistance in a particular strain of pathogen Stenotrophomonas maltophilia. To quote their article

“The wide utilization of biocides poses a concern on the impact of these compounds on natural bacterial populations. Furthermore, it has been demonstrated that biocides can select, at least in laboratory experiments, antibiotic resistant bacteria. This situation has raised concerns, not just on scientists and clinicians, but also on regulatory agencies, which are demanding studies on the impact that the utilization of biocides may have on the development on resistance and consequently on the treatment of infectious diseases and on human health.”

An article from way back in 1984 found that Operating Room soap became colonized with a pathogen, serratia marcescens, because that pathogen was not susceptible to triclosan, so it’s hardly like this is a new issue.

Even if you manage to stay out of the hospital, and don’t use the antibacterial soaps with Triclosan yourself, it may get to you anyway since grey water irrigation is becoming more and more common and triclosan is often present in the grey water.  It can then get into plants and into the food chain.

This is a brief article in Mother Jones about  the controversy surrounding triclosan.  It’s the same story of moneyed interests versus public good, as we’ve seen in certain medical device and pharmaceutical issues.

This article from a few years ago, also from Mother Jones give a number of facts about germaphobia in the United States.  I’ll include a few here.  So, first do not harm.  Wash your hands often and well throughout the day, but stay away from antimicrobials and hand washes.

Triclosan, the active ingredient in many antimicrobial soaps, has been detected in women’s breast milk and 58% of US waterways.
Poison centers counted 9,600 kids under 6 who ingested ethanol-based hand sanitizer in 2006, a 24% increase over 2005.
Australian doctors have treated kids’ eczema by giving them “dirt pills” containing good bacteria.
A 2007 study found that adults who regularly use household cleaning sprays are 30-50% more likely to develop asthma.
Pediatricians prescribe antibiotics to more than 50% of kids who complain of sore throats.
The Lancet reports that American doctors order antibiotics for 80% of patients with sinus infections—usually caused by the cold virus.
Penicillin-resistant microbes first appeared in 1947, 4 years after the drug was released. The antibiotic was sold over the counter until the mid-1950s.
In 1974, 2% of staph infections were resistant to antibiotics; today, more than 60% are.
Methicillin-resistant Staphylococcus aureus (mrsa) infects nearly 95,000 Americans annually and kills more than 18,500.
85% of mrsa infections are linked to health care facilities.
New Mexico governor Bill Richardson, who holds a world record for handshaking (13,392 in 8 hours), never uses hand sanitizer: “You’re going to collect bacteria just by existing.”

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