A Gracious Tone. Your resignation letter is not the time to air grudges, take passive_aggressive shots, or otherwise be unpleasant. Regardless of how you feel about your (soon to be former) job or your boss, this letter should be an exercise in professionalism and graciousness. An excellent way to do that is to say a simple "thank you." Even if you hated your job, you got something from it at some point. Focus on that positive bit if you need to.
And sure, this could be an email (all of the same principles would apply), but a letter makes things official in every sense. It also gives you a prop to take along to the face_to_face meeting with your boss, when you let him or her know that you're leaving.