Best ereader for managing large collections?

[liketheriffle.livejournal.com]

I have around 4,000 + fanfiction ebooks saved on my computer, and while I already have two ereaders capable of holding all of them, (the Kindle Fire and Nook 1st Gen,) neither of them make it easy to keep track of all of the stories on there. I want to know if there are any ereaders out there that either have a large internal memory, or the option of upgrading storage, and also have the ability to manage a large collection. I'd like to keep the cost at $100 or lower, and I don't mind buying a used ereader. Thanks to anyone who replies.