Salmonella is a type of bacteria that can cause severe diarrhea illnesses. The most common places you'll find it are in raw or undercooked chicken and other meats (a good reason to keep your hands and cutting/cooking surfaces clean). Sometimes, salmonella contaminates vegetables, getting at them through the dirt. When this happens, it doesn't really get inside them — it's on the skins. In this case, the best way to prevent illnesses is to thoroughly wash all of your fruits and veggies, even if you aren't actually eating the skins. Most people don't realize that they should wash their watermelons! If you're traveling in a foreign country like Mexico, peel everything — even grapes.
Now, salmonella does sometimes wind up in prepared products (like the recent outbreak from Veggie Booty). There's no need to drive yourself crazy worrying about this sort of thing. The government keeps pretty close tabs, and that's what recalls are for — to protect you.