What is the best way to wash vegetables and fruits?

First and foremost, we would recommend that you aim to avoid pesticide exposure by purchasing certified organic produce whenever possible. Government regulations prohibit the use of pesticides in the growing of these fruits and vegetables. You can learn more about pesticides and produce from the Environmental Working Group’s 2014 Shopping Guide to Pesticides in Produce. 
Importantly, organic produce still require thorough washing to avoid bacterial and other contaminants.
As background, researchers have found that washing under running water, and scrubbing with a brush when appropriate (i.e., produce with hard rinds or thick skin), not only helps remove dirt, bacteria, and other microorganisms, but it also helps remove residual pesticides. 
For instance, studies conducted at the Connecticut Agricultural Experiment Station compared pesticide removal methods on 196 samples of several different fruits and vegetables. Some were rinsed under tap water; others were treated with either a 1 percent soap solution or a fruit and vegetable wash. Tap water significantly reduced 75% of pesticide residues, and it worked as well as soap and wash products.
The Food and Drug Administration actually recommends avoiding the use of soap, detergents and fruit and vegetable washes because many types of fresh produce are porous and could absorb these chemicals. 
It is worth noting that at least one study has reported that a natural solution of vinegar and water (1/2 cup distilled white vinegar per 1 cup water), followed by a clean water rinse, has been shown to be more effective than water alone, and can reduce bacteria by 90 percent and viruses by about 95 percent.
The Environmental Protection Agency has indicated that a water rinse is more effective at removing contaminants than soaking since running water has an abrasive action that soaking does not have. Furthermore, they note that not all pesticide residues can be removed by washing; therefore, peeling non-organic fruits and vegetables when possible may be prudent. Also, discarding the outer leaves of leafy vegetables is important prior to washing. 
Finally, don’t forget that the health benefits of a diet rich in fruits and vegetables outweigh the potential risks of small amounts of pesticide exposure.
References
Environmental Working Group. 2014 Shopping Guide to Pesticides in Produce. Available at: http://www.ewg.org/release/ewgs-2014-shoppers-guide-pesticides-produce. Accessed on June 30, 2014.
Environmental Working Group. Frequently Asked Questions About Produce and Pesticides. Available at: http://www.ewg.org/foodnews/faq.php Accessed on June 30, 2014.
U.S. Food and Drug Administration. Raw Produce: Selecting and Serving it Safely. Available at: http://www.fda.gov/Food/ResourcesForYou/Consumers/ucm114299#prep Accessed on June 30, 2014.
Connecticut Agricultural Experiment Station. Removal of Trace Pesticide Residues from Produce Available at: http://www.ct.gov/caes/cwp/view.asp?a=2815&q=376676 Accessed on June 30, 2014.
Lukasik J, Bradley ML, Scott TM, et al. Reduction of poliovirus 1, bacteriophages, Salmonella montevideo, and Escherichia coli O157:H7 on strawberries by physical and disinfectant washes. J Food Prot. 2003 Feb;66(2):188-93. PMID:12597475

U.S. Environmental Protection Agency. Pesticides: Health and Safety. Available at: http://www.epa.gov/pesticides/food/tips.htm Accessed on June 30, 2014.

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