Case #2: you have your GPS maps in a SD card, but the GPS app only recognize content on the C: drive.
Case #3: you want to back up your files, but they are scattered every where, such as C:\MyData, C:\users\john\Documents, D:\MyData ... .
Then simply go get Link Shell Extension. With this great little tool, you can make any folders and files to appear at any more locations. For example, if you want to let D:\MyData to show up at C:\MyData as in the above case #1:
You right click on D:\MyData and select Pick Link Source:
Then right click on C: and select Drop As Junction:
That's it, now MyData folder appears on your C: drive:
Note: you were not making copies, you only made a "pointer" pointing to the original place. But to applications, such as your GPS app, they do not know your trick and they really think the folder is at the new location.
This is not a normal shortcut that can only trick you (the user) but cannot fool applications.
As for the case #3, you pick up all the folders and drop them into a single folder. Then when you back up this single folder, all your files and folders are backed up.
[update 03/25/2014] Windows 8.1 protects the C:\Program Files folder, thus you cannot use LSE to make a junction or symbolic link in it. You must use the mklink command instead. For example, if you have your GPS maps in D:\GPS, but you want it to appear in C:\Program Files\GPS (or whatever name, in whatever sub folder), you open CMD Prompt as administrator and type in:
mklink /j "c:\program files\GPS" "D:\GPS"