The May issue of WIRED magazine recruited JJ Abrams as the guest editor. A year in the making, the "Mystery Issue" features a one-issue redesign directed by JJ, with mind-boggling puzzles on almost every page and hidden clues "that are not apparent at first or second glance."
This means that while many of the articles and puzzles are available online, you will need to get the magazine to get the full Easter egg experience.
Either way, be sure to check out the JJ Abrams article on mysteries and spoilers (spoiler alert: spoilers are bad, mkay?), and the "between-the-pages" interview below.
By the way, the "Mystery Box" on the cover refers to a very funny speech that Abrams gave at the TED conference in March 2007.