The art of filing

How do you manage your paper and digital documents at work and at home? What is your filing strategy? Do you save everything? Do you have a complex filing structure, which you maintain closely?
Mindtools has an interesting article on "The art of filing". It's well worth the read. It helped me to evaluate my filing strategy.
However, there are two points I'd like to discuss further:

1. One advice is to "Store related documents together, whatever there type". I agree and it's also my practice. But a file type I missed is "email". Nobody stores their email together with the other related documents. This is interesting, because it costs the knowledge worker a lot of time. Email contains very important context information. It contains information about actions, for instance. And can answer the question: who did what to the document. So we keep email in Outlook (or whatever email app you use) and store our documents in Explorer, on a share or in a document management system. So, we are de-contextualizing our documents. And loosing important information about the documents. Or at least we're making it hard on ourselves to search for the emails that are/were related to the document and vice versa. And this brings me to my second point.
2. There's another type of document that I missed: paper documents. Yes, usually printed versions of the digital document. But with our annotations. Important annotations, which depicts what we thought of that part of the document at a certain point in time. Of course the "tickler system" is mentioned. (For more on the tickler system refer to "Getting things done".) But now we're not storing our documents in one place, are we? We now have two places to store documents, one for paper and one for digital documents. This also causes problems for knowledge workers. "Where did I store that document?" "Is the digital or the paper document the latest version?" Etc.
   

For point 1 I don't have a solution. Save the specific emails in Explorer with your documents is not a solution. So, most people save the emails with documents (attachments) in Outlook, which doesn't seem to be the perfect solution either (- not to mention the Inbox size limitations...).
For point 2, there are solutions, but they're not real solutions. Some people say: scan all your paper documents! Or use 'track changes' or 'comments' for annotations in digital documents, instead of annotating on paper documents. Both don't seem to be the real solution, because hardly anybody does it.

So I'm wondering: What would your strategy be on these issues?