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For reading papers, I rotate to landscape mode and use fullscreen (that's why I wrote it!), then zoom to cut off the side margins. Makes it about 90% of the size of the printed version, and I can read both columns at once.
Of course, wpd's column viewer is really nice and even easier to use.
As for managing files, I just use bibtex, with all my entries in one big file, and I use JabRef to manage them. What's nice is, it can import ISI-exported reference lists. No typing!
For keys I usually use year, followed by the first author's last name, and then a number if that's not unique: 2005Chen, 2005Anderson1, etc.
Then I can put the files in any folder structure under a single directory, and JabRef can find them by name (since the name is the same as the key).
Unfortunately, I haven't figured out a good way of taking notes yet. I don't like writing on the files directly, I like to have all my notes in one place. My current approach is to have a notes file in LyX where I take notes on each article as I read it. This has pluses and minuses, but it's the best method I've found so far...
I do my academic writing in LyX. If you haven't tried it yet, you should!
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