tranglos, you always bring up good discussions!
As you and many here do, I've also had to come up with a way to avoid using the default file storage that has been in Windows for the past many versions. To make a long story short, I'll summarize what I do:
--I keep all my files on a separate hard drive. The OS and program files are on the C drive, nothing else. That being said, I don't remap anything. I did that once, but when you make it "official" like that, programs start creating their own directories and adding files you don't want. I don't like that. I let the programs make their directories in the default My Documents location and I just don't care, because I don't use that folder. To make up for the fact that I have to switch to my own folders for every "open" or "save as" dialog, I use a program like Direct Folders that makes that a breeze.
There have been a couple of threads here about this in the past, I'll try to find them:How do you organise your 'My Documents' folder
That's where I first read about how mouser's system of storing files. When I built my computer last January (see this thread
) I had a very extensive off-line discussion with mouser where I grilled him on his whole method, which I really like and adopted. I even made a chart or something out of it, but I don't know where it is. If I find it, I'll post it. The things to consider here is to make sure all your files and settings are in a place where you have easy control over them. Also, how you backup affects this. There's a lot of thought that goes into this that people don't normally think about.
But I just want to emphasize that I don't do any actual remapping because, well, I just don't want Windows or any programs knowing where I keep my files and messing around with them. Yeah, just like the media libraries you mentioned...there are a lot of programs that have ideas of what to do with your meticulously organized files.