I have mixed feelings on the Due price.
As a customer, of course I want the lowest price I can get. When I saw Mouser had a low price, I immediately ordered 2 pieces. I didn't know if it was a promotional price or just a mistake. Since Tim (a.k.a. "MOUSER_EMBEDDED") posted the link to Mouser's order page, and Tim appears to a salesman from Mouser who has never contributed meaningfully to any conversation, I didn't feel too bad about taking advantage of the low price. I see it's now $48.95.
As someone who makes arduino-compatible boards, I actually think $49 is probably a pretty reasonable price for Arduino Due. First of all, they're making the boards in Italy, not China, and they're doing things like zero carbon footprint. At substantial volume, those aren't horribly expensive, but it's also a choice that locks out the absolute lowest possible cost production. Second, Due has a high-end ARM microcontroller and a LOT of parts on the board, plus a fairly large PCB built with a mix of surface mount and through hole parts. Looking over the schematic, they clearly went for a reliable, low-risk design rather then trying to optimize for low cost. For example, the 74LVC1G125 buffer between the 16U2 and the SAM3X could probably have been a couple resistors. Third, they are spending pretty substantially on engineering and also community building projects. Fourth, there is "healthy" profit margin for their resellers.
When the inevitable cheap Asian clones appear, it's a pretty safe bet they won't be incurring those costs. Well they'll probably incur #2, since they'll likely just copy the design verbatim, not even making the simplest of cost reductions like replacing that '125 buffer with a couple resistors. But they'll be using the cheapest/dirtiest Asian fabs, not spending anything on engineering or community (and they'll send all their customers to Arduino's community for support), and probably selling direct on ebay. Even then, Due isn't an inherently low-cost design, so I don't think we're going to see really cheap clones.
The SAM3X8E (sans errata) is a really amazing part. A built-in 480 Mbit/sec USB PHY is something very few other chips have (but how fast is really runs with software overhead remains to be seen). The SAM3X has a large flash memory and a pretty substantial amount of on-chip RAM. It's Atmel's largest, most expensive SAM3 part.
Then again, as a customer, the $35 + SD card price of Raspberry Pi is pretty appealing. Speaking only for myself, I would be hesitant to make any new hobbyist-oriented board that sells for more that $35.... but then I don't have a tremendous brand like "Arduino".