Keeping track of files
There are two kinds of files you need to keep track of: those related to current affairs, and those you archive for possible future use. These have different usage patterns, and may need different kinds of handling.
Current files (also called "pending and support") are for active projects. You may need to access these files at a moment's notice, so they should be at hand.
Archived files are needed rarely, possibly never. Access times may be longer, but it should still be easy to find them. An archive is useless unless you can find things from it when you need them.
Files may be digital or on paper. You may have current files on your computer, and on paper, and ditto for archived files. This might not affect the way you organize them: much of the organization is dependent on naming and sorting, and it is probably best to use the same naming system for both digital and paper files.
You may have other things than documents you need to keep track of for some of your projects. For example, one of your projects might be to move some artwork to a different country, and the artwork would then be part of your current files. Since large paintings are hard to keep on your desk, never mind risky, you may want to represent them in your GTD system using proxies: instead of putting each painting in your "current files" folder, you can put a photo of the painting there instead, and store the actual artwork somewhere safe.
There are any number of ways in which papers and computer files may be organized. For example, Allen recommends using manilla folders for papers, and dislikes hanging folders; others like hanging folders. If nothing else, hanging folders seem to be easier to find in at least some European countries, whereas manilla folders are considered an exotic American delicacy, which cost a premium.
Some people reject both kinds of folders, and use ring binders. Or envelopes. More important than the physical manifestation of the concept of "folder" is how you arrange them, when you have many of them.
What seems to work best for me is to have an easy, cheap way to have very specific folders (envelopes, tabs in ring binders, whatever). Each folder should have very specific kinds of items in it. Thus, a folder named "Edinburgh council tax, 2011" would be better than "Financial stuff". The former is very specific, the latter would quickly grow to be unhelpfully large.
Every folder should be labelled clearly. People with a lousy handwriting font might want to invest in a label writer of some sort, so that the folders can be labelled in a readable fashion. However, clear handwriting, if you have it, works fine too.
Allen recommends a simple alphabetical sorting system for folders. Others like two or three levels of keywords. Thus, the tax folder from above might instead be called "2011, tax, council, Edinburgh" or "UK, Edinburgh, council tax, 2011". The order of the keywords depends on how you're most likely to search for them: put the year first, if you think of things mainly in chronological order. Put the location first, or the words "council tax" (or "tax, council") first, if those are what you look for first. Whatever works for you is best.
You'll eventually gather a fair number of folders, so putting some thought into your naming scheme ahead of time helps a bit. However, if you've never done this kind of thing before, be prepared to re-do it at least once. ("Be prepared to write a prototype, since you'll make one anyway.")
For digital files, having a computer that can quickly do full text searches helps a lot. Indeed, you may be tempted to rely on search only, and if that works for you, great. However, there are files for which full text search won't work, such as images, audio, and video. Thus, it is probably best to put your digital, archived files in folders named using the same system you use for your paper files.
I recommend having a folder named "Archive" (or something similar in your local language), which is the location where all your archived files shall be. Under "Archive", you'll create a folder for each topic: these are the folders that correspond to the physical manilla folders (or equivalent). Have only one level of these.
$HOME/Archive/ Council tax 2011/ Debian DPL plans/ Orange GSM prepaid/ Talk: Debconf 2010/ Three GSM prepaid/
Having only a single level of archive folders makes it easier to look for them manually, when full-text search is not available or isn't good enough. If you create folders within folders, searching manually becomes at least an order of magnitude harder.
Create a folder under "Archive" even if you're only putting a single file there. Later you might need to archive a second file together with the first one, and if you didn't create the folder beforehand, you'll have to move the first file.
The archived files should be left undisturbed. Do not modify them in the archive. If you need to start changing them, move them out of the archive first, into your current files. It's OK to read from the archive, but not change them.
Scanners and shredders
Paper is big and heavy and hard to grep through. Scanning everything you put into your paper archive makes it possible to carry it with you on your laptop, and often makes it much faster to find a particular item, particularly if you can get OCR to work so that your scans result in text rather than images. Further, you can more easily make backups of your digital documents than of your physical ones.
Scanning everything also often gives you the option of shredding or recycling stuff you don't actually need in hardcopy. This is even better, since it allows you to reduce the size of your physical archive. That, in turn, means it takes up less space (reducing living costs, since you can have a smaller home), and makes it easier to move.
However, before you shred, be sure you do not need the physical copy. In some countries, tax authorities require the original physical document or receipt, for example.
Many devices come with manuals in many languages. Often it is possible to find a PDF of the manual from the manufacturer's website, allowing you to get rid of the bulky manual.