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I believe that with the new salt and pepper shakers, the salt shaker is the one with 3 holes, while the pepper goes in the one with 2 holes. Salt is used more than pepper anyway. Pepper should only ever be fresh ground at the table, meaning salt shakers win out.
Credit: Elizabeth McClay CC-BY-2.0. The traditional debate over salt and pepper shakers involves the amount of holes. In Europe, the pepper shakers often have more holes. However, salt shakers in the U.S. typically have more holes than pepper shakers. This reflects the value of the different spices. Salt is more common in the U.S., while pepper is valued more in European dishes.