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.
Turning in your two weeks notice can be terrifying__because no matter how well you think you know your supervisor, you can never be 100% sure of his or her reaction. Will he be furious and insist on walking you out the door immediately? Will she beg you to stay, enticing you with an enormous raise? Or will he be completely civil and wish you the best of luck?