On my system, %AppData% leads to ApplicationData which is C:\\Users\\
But there is also C:
According to MSDN the difference is that LocalApplicationData stays on the local machine and does not roam... ApplicationData does roam for example if the user logs onto the domain from a different computer it will be synced...
The LocalLow refers to specific situations likea BHO running in "Protected Mode" of IE...
For a standard application always use ApplicationData. Use LocalApplicationData for things that should NOT roam with the user...