I used to use manila folders but I found that to be way too cluttered to look at with pieces of papers sticking out in mumble-jumble form plus I had problems with tiny scraps of things not really staying put in the folders.

Since this year, I've started using envelopes and writing the subject (i.e., "Ford Explorer 1994" refers to our old SUV and contains all papers relating to this vehicule including registrations, transfer of ownership, sale, old titles) in the upper right corner. The envelopes are filed landscape and the open flap is tucked into the envelope so I have easy access to the contents. It's made for a less cluttered look and it's so much easier to find stuff -- especially given that nothing is in alphabetical order. Just the most recently accessed folder is filed in the front of the box.

This is a variation on the Noguchi filing system. Unfortunately, the best reference to this system (http://www.lise.jp/honyaku/profile.html) is temporarily down.