I think stacking windows make more sense in the context of the pre-OS X Macintosh UI. The Mac was built entirely around the concept of spatial manipulation. When you opened a folder, it would remember the exact position and size of its window, where all of the icons were, where your scroll bar was, whether the folder was set for icon, list, or detail view, etc. Every window was permanently and unambiguously associated with a single folder. This made navigating the computer possible entirely through muscle memory. Just like you know where all the light switches and doorknobs are in your house after a few months, you would gain the ability to navigate through files on your computer extremely quickly because when you double click on a folder you already knew where it would open and what would show up in the window. Instead of remembering a file path, you would remember a series of mouse motions to get where you wanted with very little conscious thought. Obviously this workflow isn't suitable for everyone, but a lot of people enjoyed it and I think it's a shame that Apple decided to throw it out for Mac OS X.

Another feature that gets a lot of flack from some Linux users is desktop icons. This is something else that a lot of UIs screwed up (maybe stemming from Windows 95? I'm not sure). The classic Mac UI let you drag whatever files you were currently working on to the desktop and do whatever you needed to do. Then when you were done with the files, you could highlight them and select "Put Away" and they'd all get moved back to their original locations. The desktop was a temporary space for what you were actively working on, not a giant catch-all storage location like how modern UIs treat it.