We buy all of our's through either Fry's or Circuit City.  We stumbled across the 20th Anniversary set at Best Buy in Arlington, Texas by accident.  They didn't have any of them on display out front (I guess it interferred with whatever mass garbage came out that day which seemed to last the next two weeks... probably Iron Man or whatever).

Anyway, we asked the salesperson about the Mystery Science Theater 3000 20th Anniversary boxed set and the guy said he'd look in the back. They had a whole box of them back there that had never been opened! I'm guessing that they're hording them for the holidays or trying to save them to scalp on eBay next year.  I can't think of any other reasons they'd have the set sitting in storage rather than taking up a corner of a display shelf out front where they can actually generate sales for the store.