Back to the original question.
1. On a large external hard drive, I keep the master copy of each eBooks. I use the operating system's normal directory hierarchy to keep up with where the book came from:
/eBooks
2. I copy the master directory with all its subdirectories onto a 2G thumb drive that lives in my backpack. So far, it's been big enough to hold all the books I've downloaded. At some point in the future, it will probably have to be limited to books I'm likely to read "soon".
3. I transfer active books into the main memory of the Kindle and put the potentials and already-read books onto the 2G SD card in the reader. Since the Kindle doesn't support directories, the books are simply "there". Before I start to read a new book, I use the Kindle's content manager to make sure that the book I'm reading is in main memory. (I've heard that it runs the battery down faster to read directly from the SD card.) Periodically, I delete the already-read books from the Kindle unless I think I'll read them again soon.
4. I maintain a couple of text files in my laptop:
* All eBooks
* Books I want to buy/read; both p and e
* Series lists; one per author
* Master list of books read
* Books read in 2008
I transfer these to the Kindle, updating it periodically.