About point 2: I do not know how this works with iPods, but my sony touch automatically assumes each 'tag' is a catagory. In a way, through those tags I am able to create catagories, at least on my reader, much like I'd otherwise use folders (I, too, was looking into a way to create those, but alas, no dice).
I store my library on my server by the way, with a network drive pointing to it - this pretty much means I don't have to also keep a local copy. Of course, when not at home it's a bit trickier to set up a VPN, but I'm not sure if it'd be easier or harder than switching repositories.
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