I don't bother with Calibre or anything similar; I simply use the directory structure. Easier to show it with examples than explaining it.

You get the idea, right? No additional software needed, any automation tool to move/rename files can be used to help you out, and since metadata isn't used for the organisation you can take your sweet time checking and fixing it. And sharing it across my network means simply sharing a directory with everything in it.

Key points to use this approach effectively:

1. Keep it simple. If you need to think on where an item should go, you're probably over-engineering your sorting.
2. Keep it objective. For example, genre is usually a bad sorting criterion, as the same piece of media can belong to 2+ genres. Author, franchise, set (season, album, etc.) are typically better.
3. Keep it flexible. It's fine and good if each subdivision has its own sorting criteria. Just be consistent with it.
4. Keep it accurate. Names are part of the sorting structure, and should be descriptive.
5. Keep it clean. Don't add unorganised items to the file structure; if you must, keep a separated "to sort" directory elsewhere.
6. Keep it broad. You're probably already used to this due to the Johnny decimal system, but broader categories are usually better. Just don't create artificial divisions to arbitrarily nest divisions, though; remember #2.
7. Keep changing it. Ultimately the goal of a sorting system is to find your stuff; it is neither to be a control freak, nor to follow the advice of some random internet person like me. So if something is not working well for you, change it.

Ah, on automation:

• GPRename and Bulky are useful to... well, bulk rename files.
• EasyTag can do it for audio files, based on the metadata and/or info retrieved from the internet.
• Wikipedia "$series_name list of episodes" for descriptive names for anime or live action seasons. Often you can copypaste the whole text bloc into a text editor, and use some find-and-replace to get rid of everything except episode number + episode name.
• Calc (yup, the spreadsheet program!) is a godsend. Specially with the above, plus a terminal; it means you can create on the spot a bunch of commands like

mv 01.mkv "01 - The Sphere.mkv"
mv 02.mkv "02 - The Inhabited.mkv"
[...]