Thanks for the responses.
=X=, it'd be need to read your writeup about syncing non-Amazon .mobis on Kindle. Concerning .pdfs, are you talking image-based files or reflow? I often download Google Books pdfs of old materials and mark them up in PDF Annotator on my TC1100, but I've been skeptical that these books would work well on my little NC screen. Reflow, however, might be a different story. Are you saying that you can markup reflowable PDFs and have those annotations available on a desktop program?
murraypaul, interesting idea, I'll have to think about that one. Not an elegant solution, but I suppose it would work. Again, interesting.
I will say it is a little sad if word processing files are the best we can do with the current state of e-reading.