I have a large PDF collection - and several applications that claim to help me 'manage' my PDFs.

Some are focused on being note-taking tools; some see judicious selection from your PDF collection as research fodder for the writing process (Scrivener, Selenium); others are interested in organizing and mobilizing reference metadata for citation while writing papers (Reference Manager, RefWorks, EndNote); others have only added file management to robust citation management (Sente, EndNote) or vice-versa (Zotero).

And then there's Papers. Hands down the best document + metadata search, retrieval & article management app for the mac.

No Smart Folders made by Tag Folders show any contents, even after "successfully" tagging files. Using other means, verified that OpenMeta Tags are attached: TagFolders' Smart Folders just aren't showing any contents.

The upshot is; I can get the TF Smart Folders to function, but my fix occasionally causes the Tag.app they belong to stop working. For details, read on...

My Work folder is for the documents that I (or any collaborators) produce for specific projects. The important organizational idea here is just identifying the area of my life to which these documents chiefly pertain.

This used to be a lot worse than it is now. On its way now, but there are still some big question marks.

As mentioned in a previous post, you find my Work folder in ~User/Documents. Inside, my Work folder is broadly segregated into context areas: AS, clients, education, GRS, employment, projects, MRB.

Okay, (small rant to follow) does it bother anyone else that app-makers interpret Apple's guidelines of limiting the locations of application-written files etc. to 'Application Support,' 'Preferences,' or 'Documents' as 'put everything in the damn Documents folder?'

Its just kind of anti-social behavior on the part of developers makes it hard for users to keep documents in their Documents folder. I, for one, have done my best to keep non-documents out of my Documents folder. Microsoft apple division, I hate you for putting 'Microsoft User Data' in my Documents folder. you suck. Keep your nasty data files where they belong. And you others...you know who you are. Shape up.

Seriously, guys, if something is a database app, like DevonThink or Delicious Library, what is documenty about the database file itself?!? (More, and more serious stuff, after the break..)

As a sidebar to my discussion of my strategies for managing my Applications folder, Ill answer the question: Whats with these Stack 'Drawers', anyhow?

A 'Drawer' is used to visually brand any Stack with a nifty customisable icon that remains the first item in the Stack regardless of how many new items are added to the Stack's folder.

But first: Why would you want to do all of this?

These simple steps allow users to visually customize and thus (hopefully more easily) differentiate among the Stacks in their Dock.

Here's how:

Actually this one is usually, mostly all right.

My desktop is my landing pad for my own work, or stuff I grab from the internet that requires special handling (like renaming, tagging, filing, conversion, analysis etc). Like when I want to quickly make an icon for a new concept I am trying to represent and grab some images from the web as conceptual resources; or for PDFs, Word documents, and other stuff I've dragged from my Downloads folder to work on before filing.

Desktop Shortcuts are the enemy! And so is a mess of files...

My desktop is most often empty. This is my ideal.

When I have to keep this project or that in mind, ill sometimes drag an alias (or the project folder itself) to the desktop. Its being there irks me just enough to provide an extra nudge towards completion.

Okay so this one is not *really* so bad. But its easy to get out of the sweet zone with this one, too.

I recently switched from a 'multiple-custom-folders-inside-the-Applications-folder' to a single custom folder inside the Apps folder. Ask me why...and we'll test your threshold of pain-tolerance, geek style.

OMG. What a nightmare. Of course, I'm mostly trying to build my collection of tools, so 99.8% of my downloads are applications.
As in the case of bookmarks, I can tell you that simply having accreted a directory structure (slowly over time) is *NO* guarantee that the folder structures that I used to file "Little Snitch.dmg" last time will be the one that occurs to me next time I have download an updated disc image of that app.
So how do I get past this endemic classification continuity/consistency problem?

Ok. Ill admit that at one point in time I was assiduous about filing my bookmarks.
As all 'filers' do, I quickly ran into problems, though. In an ideal world, with a highly 'curated' filing system, each folder would *ideally* become like a keyword for 'finding' the bookmarked resources again. Except that firefox does not search the directory names when searching thru your bookmarks. Seriously?!? Big flaw, but true.

My email inbox. Sheesh. You'd think that after spending hours. ..no, DAYS creating and tweaking rules for Mail.app, you could have a set-and-forget, self-maintaining inbox. But...Nope.
Especially since on a mac, you first need to put in all the effort of adding the addresses of incoming messages to your Address Book.app and creating groups (to be used by Mail.app rules).
But...No. Still a mess. My inbox ends up as the place where everything that 'slipped through the cracks' of my extensive rule-list ends up. I think I clean it up every 4 months or so. On a semesterly basis. I currently have about 300 500+ unfiled unfortunates in there.