When it comes to infectious agents, like bacteria, viruses, and fungi, cleaning is an important way to reduce their spread. What people are really trying to do when they wash their hands or wipe a surface is reduce the number of pathogenic microbes present. In reality, all surfaces, including the surfaces of the human body, are teeming with microbes, most of which are just minding their own business. The pathogenic (disease-causing) ones are just a small percentage, but they're increased in number in places where a sick person has been. Washing and cleaning reduce the chances of getting sick from a pathogen because they get rid of as many microbes as possible, including the bystanders.
Washing with soap is more effective than washing with water alone because soap can remove sticky substances, including bacteria. Plus, the completeness of cleaning (measured in the percentage of bacteria removed) increases with the length of time that you lather. But is washing with antibacterial soap any better?
Antibacterial soaps have a low concentration of phenol-containing chemicals (like Triclosan) that disrupt the cell membrane of bacteria. The concentration of Triclosan in soap is too low to kill bacteria, but in theory, because its activity lasts for a time after you've washed your hands, it should be able keep bacterial numbers down longer than regular soap should. But when it comes to reducing bacterial numbers on hands, tests have shown that washing with regular soap was equivalent to washing with antibacterial soap after a year of regular in-home use.
One important question is whether Triclosan-containing products cause increases in Triclosan-resistant genes in bacterial populations or, even worse, cause cross-resistance to antibiotics? Laboratory tests say yes, but this is hard to test in everyday life because people also take a lot of antibiotics. Manufacturers of antibacterial soap aren't yet required to show that their products are better than regular soap and water, but the U.S. Food and Drug Administration (FDA) has proposed to require them to do so. In addition, the FDA wants to require manufacturers to show that their additives are safe for daily use, which they aren't required to prove at present.
Hand sanitizers have a high concentration of alcohol and work better than soap when it comes to remove bacteria and viruses from skin. Instead of targeting a specific microbial component, alcohol messes up protein structures, which are part of the outer membrane and cell wall of all microorganisms, as well as your own skin cells. This means that they inactivate microbes in a nonspecific way that won't lead to resistance. They aren't effective, however, against bacterial endospores or non-enveloped viruses, both of which can cause the nasty diarrhea and vomiting outbreaks that are common in the winter months. Also, in order to completely eliminate microbes, the alcohol rub has to cover all surfaces of the hands, requiring about three squirts of the product each time (which is more than many people use).
So, it seems that the best way to remove pathogenic microbes on your hands is to use alcohol rubs when you're on the go and good old-fashioned soap and water when you're at home. Antibacterial products haven't really been proven more effective than regular soap for cleaning, and their risks are largely unknown.