I don't think applications will be as much of a problem as you think. As with a lot of open source hardware project it's only a matter of time before you'll have a community backing it. That means, a lot of the Linux applications will be ported over.
Also as another benefit of this using an ARM processor and a lot of netbooks and other hardware going the way of Linux this is good for the OS side of things. Windows won't go away and I wouldn't wish it to as it has it's place in the computer market, but getting people away from the Microsoft way of doing things is a good thing. Either through Apple's hardware or these open source hardware projects will slowly eat away at Microsoft's market share. It's an uphill battle and won't be over anytime soon but I like where it's heading.
