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I used a file structure to manage my ebooks for many years. Only using Calibre from the command line for format conversion. It works well enough, particularly on ebook readers (now rare on mainstream EInk devices, still available in some apps) that explicitly supported folder navigation.
When I switched from an ePub reader to Kindle I started using Calibre as a library, initially only to do bulk converts to MOBI. But I found it could do much more. For a Kindle 3, the collections plugin can completely automate collection management and sending new ebooks to the device is simple with Calibre. There are more things to fuss with in the library, like covers and metadata and accurate series info. They take a while to get right for large libraries, but they are well worth the effort. This does not take long when adding new ebooks, but it is a time sink if you switch to the Calibre library with an existing set of ebooks. This is all optional, but (for example) searching book description metadata, what Calibre calls comments, is very helpful once you have good book descriptions.
I still maintain the ebook file structure separately (as speakingtohe suggests), and sometimes it is the easiest way to check on a particular ebook, but I find I am using it less and less. I still do my initial ebook conversion from the command line, because I have various chapter detection options ready to go if needed. Even this step is probably just as easy from within the library though.
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