I started pondering this question when I read this "10 Germ Myths" story at ABC News. In particular it discusses the myth that anti-bacterial soap keeps your hands cleaner than regular soap. It turns out to be a myth and one that is perpetuated by the lack of understanding of what one is attempting to accomplish when they wash their hands.
Now, I plead ignorance here: I never really thought too much about bacteria and my hands. I simply followed the mantra taught by all parents: wash your hands with soap and warm water to stay clean and healthy. Staying healthy implies I am getting rid of germs (bacteria and/or viruses) and thus preventing the spread of some infection. Therefore, you would think that anti-bacterial soap would help in preventing this infection by reducing the number of pathogens on my hands. It turns out that the US Food and Drug Administration has questioned this notion for some time now.
So, what happens when you wash your hands? Well, germs aside for the moment, the goal of washing your hands is to get clean. Getting clean means getting rid of dirt and grease, which is generally hydrophobic, which means it doesn't play well with water. Therefore, simply running your hands under water will not work well. It may wash away some of the loose debris, but dirt that is caked onto your greasy little hands will stay right where it is.
Something different needs to be added to this equation. You may think, "Hey, if dirt is hydrophobic, then it must like to mix with oil. Let's wash our hands with oil!" Your first thought is correct. Most things that are hydrophobic, like oil itself, do mix well with oil (lipophilic). But if you washed your hands with oil you are just compounding your original problem. How are you going to get all that oil off of your hands now?
If only there were a chemical that both liked water (hydrophilic) and liked oil (hydrophobic) at the same time. Well, let me introduce you to my friend SOAP. You can make soap by heating up some fat with some alkali/base such as Sodium Hydroxide, NaOH, or as fans of Fight Club (or soap making) call it: Lye. What results from the saponification process is a long hydrocarbon chain with a Carboxylate head, i.e. CH3-(CH2)14-CO2-Na. The Sodium ion will dissolve off in water creating a negatively charged head. These soap molecules are known as amphiphilic -- they are both hydrophilic and lipophilic.
When a bunch of amphiphilic molecules meet, they form a micelle, which is a ball of with the hydrophilic heads on the surface and all of the hydrophoibic tails in the center of the ball. This is due to the interaction of the negatively charged head with water, which is a polar molecule, and dispersion forces between the long hydrocarbon tails.
This micelle makes the quintessential emulsifier: something that can aid in mixing two immiscible liquids -- usually oil and water. When cooks think of emulsifiers, they think of the egg yolk in their mayonaisse or honey and/or mustard in their salad dressings. For soap, though, the micelle arrangement is perfect. It allows the dirt/grease to get trapped in the center of the micelle with the lipophilic tails. At the same time, the Carboxylate head keeps the center from mixing with the water (and repels other micelles, since they are all negatively charged surfaces) and keeps the dirt suspended in such a way that it can easily get rinsed away off of your hands and down the drain.
Back to Bacteria. This is a leap of faith on my part here, because I am not sure, but I assume the same process can encapsulate bacteria and wash it away. What I do know is that regular soap does nothing to kill bacteria, you are just washing it away.
Anti-bacterial soap, on the other hand, does contain chemicals mixed in with the soap that can kill bacteria. However, the aforementioned studies seem to indicate that using these soaps does not decrease the rate of infection. This is most likely due to the fact that most anti-bacterial chemicals need to be left on the skin for at least two minutes to work. When is the last time you rubbed Dial all over your hands for more than two minutes without rinsing? That's what I thought. In fact, using anti-bacterial soaps has the potential to create "super-bugs" that are resilient to said anti-bacterials (such as Triclosan) and creating a problem much worse than having dirty hands.
Alcohol gels, on the other hand, are better at killing bacteria, considered an acceptable substitute to washing with soap and water by the CDC, and will not result in the potential evolution of a resiliant super-bug. The alcohol concentration needs to be >60% to do its job properly (its job being to dehydrate bacteria to kill it), so soaps that contain alcohol don't contain a high enough concentration to be "anti-bacterial," especially if you rub your hands under the water immediately. Also, keep in mind that these alcohol gels kill bacteria, but they don't "clean" your hands in the "dirt and grease" sense of the word. You need soap and water for that.
One final thought: We learned that soap does not kill bacteria. So, the next time you are in a public bathroom (or at a friends house) and you see that white bar of soap, think to yourself: how many people have wiped their E. coli ridden butts and then used that soap? And then start carrying around some Purell.