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What are you planning on reading? How do you want to use your reading device? I don't know of any Linux e-reading software that annotates, but I'm no expert on the OS (as far as I can tell, FBReader does not annotate). With Windows, you'd have more reading software choices as well as the additional option of downloading PDF XChange Viewer for annotating PDFs. I don't think there is anything comparable for Linux (I use WINE to get PDF XChange on my HP Linux Netbook, so that's an option, I guess).
That said, I can't imagine reading anything except PDF articles on my netbook. If you're a techie, you could always spend $90 on an eBookwise 1150, which allows you to highlight text and handwrite notes with the stylus. It's quite old school--you might feel like you're in an 80s sci-fi movie when using it--but if you have the know-how, you can convert most major formats (.lit looks really good, in my experience), and transfer marked up books back to your computer. The disadvantage is that you have to use a Smartmedia card to retrieve books from the device to your computer, and you have to use a propriety software viewer to read the books on PC. It's very much a legacy device (be warned), other choices would look better and be more flexible about formats, but other readers are not $90. For great ergonomics, annotating ability, and backlit reading in bed--well, I've found the device a pleasure.
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