[tomsem]

It may be too radical for most folks, but the only things I keep on my Kindle are:
1 - books I am currently reading or haven't read yet
2 - 'subscriptions' generated by calibre
3 - 'personal' documents (PDFs of electronics manuals and technical docs)
4 - references (dictionaries, feedbooks directory, gutenberg magic catalog)

These typically comprise fewer than 40 total items, and since I usually have my home page set to view Subscriptions or Books only, I have at most I have a couple of pages to navigate. I remove anything I have finished reading immediately. Amazon purchases are automatically archived, and everything else I read is free so I can always get another copy should I wish to.

I use my computer and Kindle for Mac to find new reading material and view book samples. When I finish reading something on my Kindle, I use my computer to pick another book to read and send it to Kindle. I don't buy anything until I'm ready to start reading it.

Getting the samples off my Kindle and onto my computer really uncluttered things and helps me concentrate on what I'm trying to finish reading. I have about 80 samples, and I doubt I'll wind up purchasing more than 20% of them, but these function as sort of a wish list. (I know there's a Kindle Store wish list now, but I haven't tried that yet.)

I personally have no reason to have 'hundreds of books' on Kindle. As a matter of practicality, I can only effectively read a handful of books at a time (if that <g>), and what I have on there is enough to keep me busy reading for weeks. So this system works well for me.

If I wanted to do 'research' with it, Kindle would be completely inadequate in terms of organizing and annotating materials. I think that will continue to be the case even when Amazon delivers its 'solution' for organizing, largely because its PDF support is so limited (no annotation or link support) and PDF navigation is so slow. I will occasionally restore a book I have previously read so I can look something up, but find I don't need to do this very often, so it doesn't need to stay on my Kindle cluttering things up.