Hi there, I'm also a Mac user and have had similar thoughts lately re whether my filing system is really cutting it. I have recently started using the colour labeling system available in the Mac. The system allows you to essentially tag a file with a colour code. Each colour code is associated with a particular area you wish to define eg, Studies, Home, Client Matters, Admin, Investments etc.

The next step is to set up Smart folders in your Finder that correspond with these colour labels ( I also have mine set up with a time frame). For example, red label = Studies; Time Frame = only last 2 months), that way the Folder will only ever hold files colour coded red and that were created and/or modified in the past 2 months. The folders have less clutter in them for every day use. However when I need something older I need to dig deeper in the Finder for archived files (that is when Quicksilver is handy).

Just an idea.

I decided just to go for it, but on a small scale. For about three weeks I have been using tagging with Quicksilver's File Tagging Module. I have not gone through the process of tagging everything, and not sure that I will. However, what I have used tags for has worked wonderfully for me. I'm primarily using tags for my various active projects as a way of keeping each project's respective files "together." I'm not sure if the tagging thing would work system-wide. It's possible that too many tags could lead to a meltdown, or it could lead to salvation and puppies for all. My jury's still out on that one.

I'd love to read some other users' experiences.

One of the things I find most important about tagging via Spotlight comments in OS X is being able to have some kind of index of the tags you use. I'm a huge tagger of stuff on del.icio.us, but they've kind of gotten out of control, with a massive tag cloud (*choke*). I recommend setting up some kind of system, be it a text file as an index, of the tags you use that you can at least somehow reference.

I also use Devon Think and use directories. Haven't gone to a non-directory format, but there is an "unfiled" directory I use with a ton of crap in it that I may never just use.

Am personally on the fence with DevonThink Pro and Yojimbo. I love that Yojimbo has Spotlight integration -- the idea of it, anyhow -- though I've never had to use it. However, I enjoy aspects of DP over Yojimbo -- particularly how customized I can make the UI, how pop-up windows remember their sizes from one to the next, etc.

One thing that I've also done with system tagging in OS X is to add tags to calendar events and my address book. To do so, I make sure my tags all have some kind of unique prefix, like @clients or something. Doing a query in Spotlight then brings up not only files, but contacts, events, etc. Great way to relate items together across multiple applications.

Haven't tried the folders solution that akr95 mentions -- frankly, I think one thing DP and Yojimbo are good for over this menthod is creating web archives. There's no tool I know of in OS X (and I'll now look) that allows you to create web archives of this sort as "files" you can drop in a standard Finder directory.

The Apple Blog is running a series of posts on this subject. You might find it helpful.

Three programs you can't do without:

Journler ? Designed with GTD in mind (download it and look at the example documents), it organizes writing and various media. I swear by it. Freeware.

Yep! ? Probably what you're looking for, based on your post, to organize documents and other media. I've only started using it, but it seems to be very useful. I download a lot of academic journal articles (and e-books) as PDF and needed a way to organize them:

You may also find Yojimbo useful for day-to-day information "ubiquitous 'stuff' capturing".

I wrote about how I am doing this a while ago (Blog post it links to) but I'll offer one additional comment re: Yojimbo.

The following paragraph isn't meant to just lambast Yojimbo. I like it and hope it can overcome the problem I'm about to describe so I can keep using it!

Yojimbo sucks big time when it comes to handling large files. I have been in contact with the Yojimbo support team for months about Yojimbo choking my system on launch and at various points after it manages to get itself going. My database isn't even 1GB yet and has a little over 300 items. Shouldn't be a problem, but Yojimbo just can't deal with it at this point. I want to use it to manage all my reference information (receipts, PDF's/whitepapers, etc) but at this point I can't trust it because I can't be sure it will respond when I need it to.

Putting files in folders is a way of tagging them. The limitation is that you're only allowed to add one tag (unless you start aliasing them across multiple folders.) If you want a space-less, iTunes interface to files try EagleFiler and KIT. I know that KIT has tags now and that there has been talk of adding them to EagleFiler.
Tagging will only "blow up in your face," when you stop tagging everything as it comes in. A large back log of anonymous files will lead you to doubt the completeness of the results that are returned by your system.
The advantage of Devonthink is that it can classify and find relationships regardless of your tags.
My system is also still evolving, but I'll probably use one app to actively tag and annotate files (like KIT or perhaps Mori if the file linking is upgraded) and then DevonThink to index the exact same set of files for relationships that I didn't expect.

Though that being said, a good searching system that understands the contents of your files, rather than just the metadata, will almost always be enough to find anything you are looking for. The problem is with those files whose contents are hard to abstract or search (image files, for example).

This is true, but I guess the point I was trying to make is that the first few times you need to use a search (like Spotlight) to find the files that you didn't or haven't tagged, you'll start to question the system slightly. In most cases, that will mean one of two things: 1) this motivates you to be more vigilant in your tagging, or 2) you become a little more lax in tagging since you end up having to search anyway. If for you it's #1, great. Tagging will probably become a useful resource for you. If it's #2, your tagging system will most likely quietly implode after time.

I'm not against tagging. In my own experience, I find it's most useful for those tags that are completely unrelated to (or at least, not explicitly expressed in) the content of the item. Things like "get citation" "use for PNAS paper" "share with lab" "read" are great things to tag with because they express my relationship to the item. However, tags like "cells" "polyimide" "network biology", are not as helpful because usually that information is already encoded in the paper's content and can be teased out with Spotlight or DevonThink. This works for me because 95% of these items are journal articles in pdf format--as you mention, someone using mostly image or audio files would have to adopt a different scheme and would probably find great utility in extensive "content" tagging.

I guess I think of it like GTD's "trusted system": in order for you to really have faith in the results, you have to know that your system is completely capturing the inputs.