This is the time to think of a new way to organize your stuff. Throw away your shortcuts and organize your directories with the use of the new Windows 7 libraries. Create new libraries and collect directories in them. Don't move default windows directories - collect them in custom-made libraries instead.
There are also these "recently used" picklists in the task bar and the pinned items in the start menu. Often, it is not neccessary to directly create shortcuts - they are already there in the lists of "recently used" stuff.
Over the last years, I distributed my data under Windows XP to many different locations. Small but important stuff to a network server, big stuff (videos and virtual machines) to the local drive. Some things were partly local and partly remote. It was a mess. I consolidated all this and made a few additional libraries where I collected all important directories in a well-organized way.
A big help is the change that music, video and pictures are not hard-coded subdirectories of the "my documents" folder any more. Instead, I am able to freely move these default directories around (click properties of any of these directories and you see a additional tab called "path", which was present on XP only for the my documents folder). There is a built-in way to move these around, so you could do it. But don't move other windows-created directories around, for example program (*.exe) installation directories. Try to install applications to the default paths.
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