>> I also have folders that themselves hold a bunch of bookmarks.
Except for my "Garden" folder and "seed vendors" folder of bookmarks, most of mine are only 1-deep. But I keep re-organizing my nested seed vendor folders ... right now it's 3-deep, with my most-often visited sites in the top two.
For shortcuts on my PC, I keep a link to my main "folder with folders of links" in the "Quick Launch" part of the Windows XP Taskbar. That's by far the oftenest-clicked link on my desktop.
I like fiddling with gadgets, and eliminating one click from a chain seems like a worthy pursuit. Also, if I DO have a chain of clicks, the most-frequent path through the chain should not require much mouse movement: like the most-often-visited link should be near the top of each layer.
I'm pretty sure that the PC revolution created whole new kinds of OCD.