I got a call from EB this morning informing that my Sam & Max: Season One pre-order was cancelled because they got word from the publishers that it was no longer being made. So, is there only one version now, the one you get directly from this website?
In any case, it must be a blessing in disquise. I never knew about the exclusive pre-orders from this site (the bonus DVD, getting all of the episodes on CD) as well as all of the cool swag. I pre-ordered the Season One Collection + Bonus DVD, as well as the Sam & Max Season One Case file, Soundtrack, and Artbook. Sure, I spent more than I originally planned, but what can I say? Sam & Max are awesome, as are all of you Telltale employees. You really go the extra mile with your products, and show true love and devotion to your fans (don't worry, not in a creepy way :D). Thanks again, and I can't wait until the July release.
EDIT: Thanks to Jake, a Telltale Team Member, the above information has been proved to be false (as you can read below), as the game is still available for pre-order in EB/GS locations (just not online apparently).The retail version is not cancelled, and apologize for the misleading information.