Scion, thanks for that link; I'd missed that one.
I know you are fond of Aldiko. I also like the interface and flexibility of it, but the fact that it forces you to place your books on the SD card then appears to copy them makes this a no-go for me. Maybe I'm doing something wrong here, but part of the issues I'd experienced recently with my library (detailed in an earlier post) were due in part to the fact that I unknowingly had two copies of books and Calibre was seeing both of them.
The other issue I experienced with Aldiko -- and something that I hadn't seen anyone else post -- was the intermittent page turn delay every few pages on ordinary sized books.
Anyway, for the time being I'm sticking with the stock B&N reader. Since my entire library is epub, I haven't experienced a single issue with the stock reader.