I just received a Barnes & Noble "Nook SimpleTouch" (the basic, e-ink screen one), and while I like it, this sort of thing has me very worried about using most of its (limited set of) features. That is, while the Nook has something like 1 gb of internal storage for books, about 75% is reserved for content you have to purchase through Barnes & Noble. That leaves about 230 mb for your own files. (The Nook does feature…
Last week I finally broke down and bought a DRM book from B&N's website. It let me download an encrypted EPUB file, which I transferred to my Nook over USB. Without having to enable WiFi or register my Nook, I was able to open and read the EPUB just by entering my name and the credit card number used to purchase the book. (By the way, I only had to do this once.)
It still sucks because it's DRM, but I'm reasonably confident that with this setup, B&N can't remotely kill my books, and it should keep working even if B&N goes bust. You might want to consider it.