A video on youtube discusses a recent study that claimed to find all kinds of harmful microorganisms, including fecal bacteria, on the lemon wedges restaurants place in drinks. Microbiologist Anne LaGrange reported that when she tested some lemon wedges "it was like they had dipped it in raw sewage."
Apparently the problem is that restaurant workers often handle the wedges with their bare hands and they cut the lemons with knives they may have just used to cut meat.
David Emery of About.com has analyzed the claims in this video and finds them to be basically true. There was a study published in the Journal of Environmental Health in December 2007 which found significant microbial content on a high percentage of lemon slices from twenty-one different restaurants.
However, David also notes that health experts don't consider dirty lemon slices to pose much of a risk to public health. But if you're freaked out by the idea of germs, you might want to say no when your waiter asks if you want lemon in your drink.