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.
Spot the Signs. According to Alison Green, who writes the blog Ask a Manager, this is common practice for some industries, especially if you're leaving to work for a direct competitor. However, in those situations, you'll likely know it's coming and can prepare accordingly.