When I first got my Kindle I put everything on it then I found myself lost trying to remember what was on it. lol
I had a problem where my indexing got messed up and it had to reindex all 400 ebooks.
I now keep my library on my Dropbox and when I want to read something I use my android phone to download it then I gmail it to my Kindle from my phone. If I'm near my netbook, desktop I just email the ebooks to my Kindle.
I find this less hassle and battery then using the Kindle browser and going to Dropbox's website and downloading it directly.
I've set a limit to 50 books on my Kindle and if I lost interest in wanting to read the book a week or month later it's deleted off there to make room for more interesting ebooks.
On my older reader which is a Hanlin v5 clone it used a folder system so It had over 500 ebooks on it and I could find what I wanted with no problem. I bought a 8GB SD Card thinking I would use it up and even now it's not passed 300MB.