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.
Sure, it may sit in the depths of HR until the end of time, but you can be sure of two things: One, your former boss (and future reference) will read it and be impressed. And two, if you ever decide to come back to your company (hey, it happens), it's a very good thing that last thing on file is a great, professionally written resignation letter.