I just read this thread, and I'm quite surprised by all the comments about the kindle. Just so you know, whilst it doesn't support a tiered directory structure, once you have uploaded PDFs, you can assign them to one or more collections.
That effectively gives you one level directory, but more interestingly, allows you to group a single pdf in multiple collections, so that you can have all your aerodrome plates in one collection, all your info (plates and otherwise) about a particular location in another collection, etc.
Its very similar to the label system in google, albeit only at one level. Doesn't that go a long way to dealing with the need, or am i missing something?