System for organizing fic?

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I'm wondering what system, if any, people might use for organizing fic downloaded from the internet. Do you use Calibre? A folder structure? Something else?

I've only just started figuring things out, and while Calibre seems great for "real" ebooks, with the automated meta data, and sorting and saving by author, I tend to lean toward sorting by fandom first for fic. I'm currently using a folder system for that, which I copy onto the reader, but I can see how it might grow unwieldy if it gets big enough.

So, curious to hear what systems people have devised....

And a possibly handy tip: I recently discovered EPUBReader, which seems like a very useful plugin for Firefox.