The global settings are stored in :
%APPDATA%\Roaming\Blender Foundation\Blender for windows
~/.config/blender for linux
where there are folders for each version (2.72, 2.73, ...)
These setting can be ignored if you create a config (startup file, user preference file, bookmarks, recent files), a scripts (addons, presets) or a cache (BVHs, temporary) (or both) folder in the version folder of your installed or unzipped Blender : C:\blender\blender-2.74-rc1-windows64\2.74 \config
If the folder(s) exists and is empty, Blender will use the default settings. Global settings can be copied there and then modified without changing global settings.
Thanks to jesterKing and iKlsR