Considering that the Lion release today (which has gone swimmingly) was a vote of confidence, Apple has moved to get most of its boxed software out of the Apple Store completely, sending a notice out to retailers to discontinue titles like iWork '09, iLife '11, Aperture 3, and most of GarageBand's Jam Pack addons. All of that software will of course be available on the App Store with a download, but Apple won't be keeping them in the actual retail store any longer.
This follows Apple's actions earlier this year to remove a number of peripherals and retail games included inside Apple Stores. Much of the hardware is still available, and of course the games can be purchased with a digital download, but Apple seems to want to have its stores as clean and simple as possible.
And who can blame them? Apple's latest strategy has been to narrow down product lines and streamline software purchases with an App Store model, and that's worked out just great so far. With Lion already a solid indicator that customers are ready to take to the Mac App Store when needed, there's little if any reason left to bother with actual boxes and discs any more.