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OK, I've read your thread and maybe this will help.

In the user Documents folder, create a folder where you put all the folders you actually look at. If there are any Application specific folders that you hate that need to stay in user/documents make aliases of THOSE folders. Now drag that folder into the dock. Voila.

Otherwise, I think that maybe you just need to subcategorize your folders a little more....

EDIT: FYI, if you open word and go to preferences and then File Locations, you can change the default settings for the user data.
 
OK, I've read your thread and maybe this will help.

In the user Documents folder, create a folder where you put all the folders you actually look at. If there are any Application specific folders that you hate that need to stay in user/documents make aliases of THOSE folders. Now drag that folder into the dock. Voila.

Otherwise, I think that maybe you just need to subcategorize your folders a little more....

EDIT: FYI, if you open word and go to preferences and then File Locations, you can change the default settings for the user data.

Thanks, Mavimao, as you've seen earlier, ultimately this is what I did (except I made all of them into aliases, since at least it's a uniform ugly look instead of a mix of real and aliases).

Thanks for the tip re: Word.

Ultimately, I'll still have to experiment with jsw's recommendation on Smart Folders.

For now, I've also bought the app "Overflow":

http://www.versiontracker.com/dyn/moreinfo/macosx/23218

which helps with cleaning up the dock somewhat and is a handy launcher not just for apps, but for files and folders. I guess I just really like the dock idea (again, I think it can stand a lot of improvement, but the basic idea rocks).
 
My computer experience is mostly DOS and Windows where "attrib" is the command you'd need :) , but I'd guess that having a "hidden" attribute for a file or folder should not be impossible on Unix/OS X.

If you have the Developer Tools installed you can use the Terminal to hide files from Finder viewing: Use the Command "/Developer/Tools/SetVar -a V" plus the name of the file you want to hide. If you replace the capital V buy a non-capital v the file will switch back to visible.

In general I think the default file structure of the user home directory is not too good in OS X. There are too many folders visible, which for most users only contain a data base the users never want to navigate with the finder: Music contains essentially the iTunes data base, Pictures the iPhoto data base and Library contains lots of stuff the user never wants to navigate using the finder. Documents is somewhere in between. It would be nice to have a more consistent behaviour here like having only one folder (Library) where all these things are stored that the user does not want to browse.
 
Some playing:

Using Tiger's admittedly non-robust searching tools, you can do this:

  • Create a Smart Folder anywhere you want.
  • Set it to look only at your Documents folder.
  • Set it to show only items with a given color label.
  • Label the folders/items you want to see with that color.
  • Drag this Smart Folder to your Sidebar.

This, I think, sort of does what you want, at the cost of having to label the folders a certain color. If you click on the Smart Folder in the Sidebar, you'll see only the folders you choose to see, but there are no alias arrows... just ugly text labels.

It works but is uglier if you choose to include file types beyond just folders (or, more specifically, more than one file type).

Edit: duh, this works with Spotlight Comments as well (set the Smart Folder to look for Spotlight Comments, add a specific comment to the Get Info box of each item you want included in the Smart Folder).

This is one of the best solutions anyone has come up with so far. I also recommend that you cut down the number of top-level folders you have.
 
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