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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.
With a number of people who are already on, or perhaps should be on, low sodium diets, many argue that the salt shaker should contain the fewest holes in order to prevent overuse. Many people habitually shake the shaker without regard for the actual amount of salt escaping through the holes.