Never let the waiter or waitress take your card to the till, it's usually in those few minutes that they've swiped it into a nifty little pocket sized machine that copies the data on it, to enable them to make a clone. This movement can be disguised as wiping it in an apron 'so it swipes better'.
Always take your card to the till and always check the amount before you sign or put your pin number in. Put bold lines across the empty boxes if it's a paper receipt. Don't leave your copy of the receipt in the restaurant, take it home and file it or destroy it.
As Q says, it's impossible to protect your card 100% but you can take precautions.