One fascinating (if hard to pin down) cipher mystery that I’ve been meaning to get to grips with is the Rohonc Codex. This is a vaguely Bible-like book, written on Venetian paper with a watermark dating it to circa 1529-1540, but looks like it ought to have been written centuries earlier. And (you’ll be unsurprised to hear) nobody can read it.
Well, until such time as I find some credible source on the statistical properties of the text (which is where I’d personally want to start from), here’s a nice Passing Strangeness blog entry that describes the Rohonc Codex pretty darn well. Enjoy! 😉