It means you've done/experienced something before, or have gone through something before. For example, if you were to tell me "Hey Sage, let's go whitewater rafting this weekend, it sounds exciting!" I'd reply with "Been there, done that." (That's if I had actually done it before).
Sometimes, you can even say "Been there, done that, bought the T-shirt", just to really emphasize that you have gone through it before (because, well, when tourists visit a place they usually buy a T-shirt with the name of the place). =D