Damn! I have to share this tip
The way I organize my files, folders and everything else on my desktop, including my laptop, is that I keep all data files and everything else on a different drive than the operating system / program files. This definitely helps me in doing a very easy, click-clack-click format of my primary installation drive and be up and running fast enough with every of my data intact and all setting in place in a considerable quick time. Actually, I have a whole drive just for the program installation and another separate drive for my data files (40 GB for the Programs/OS + 80 GB for the data drive, with my current desktop configuration).
Before going further, let me add that I am on a windows box and this post is invalid for other operating system.
"My Documents" can always be assigned a different location by just firing its properties > and giving a desired target location and so also for "Temporary Internt Files". In fact, I really do not like default of a program installation. I even have my Actionscript syntax file loaded everytime Textpad starts from a different location. The only hiccup that I usually stumble upon is the "Favorites" of my bookmarks in Internet Explorer which I miss in some way or the other during a fresh installation. But today I just figured this out too and damn I am happpy to find this out, thus share the same with you.
Be warned : It is said that the Windows Registry is not to be played around and not intended for the weak heart, so back up your registry before you do that. I am not responsible for anything stupid you do. But if you follow the steps, no need to worry, everything will be a breeze.
Steps to changing the "Favorites" Folder location :
 Start > Run and type "regedit"
 Go down to "HKEY_CURRENT_USER\Software\Microsoft\Windows\Current Version\Explorer\User Shell Folders"
 You will see many other customizable folder besides the "Favorites", now change the "Favorites" folder location by double clicking on the "Favorites" value name on the right pane.
That is it, close the Registry and open a new IE window, you have your Favorites folder pointed to where you wanted. You may wish to create a folder called "Favorites" on another driver or location before doing the whole steps.