Telltale has just made a physical version of Out from Boneville available from their web site. It costs $24.99, and here's the description:
There are also bundles with the comics available. And lower international shipping. So that's pretty cool, despite all the extra material being available online (I'm assuming "promotional videos" means the trailer and the "Bringing Bone to Life" video). So buy it!
Add the Out from Boneville CD-ROM to your home game library in an attractively designed DVD slipcase. Includes complete Bone game, along with the game's music tracks in MP3 format, liner notes from the score's composer, digital collector cards and promotional videos.
And you can start playing right away! Includes the downloadable version for free!
As far as I know this will only be available from Telltale's site, however a cardboard boxed version of Telltale Texas Hold'em exists and has been found at places like Best Buy so you never know.
EDIT: Woah, check it out! Apparently if you bought the game online already you can get the packaged version for a mere $4.99. To take advantage of this offer, which expires on February 28th, just type your order number from when you bought the game into the promo code box. (Note: This only works if you've bought the game on or before January 26th.)