When you customize Maya, your new settings are stored in user preference files, so that each time you open Maya, your settings are used instead of the Maya default settings. If you delete a preference file, Maya uses the default settings.
Saving your preferences in Maya saves any changes made to colors, hotkeys, hotbox marking menus, size and position of Maya windows, and any items defined in the Maya Preferences window.
Maya stores preferences files in the following path:
\Documents and Settings\<username>\My Documents\maya\ 2011\en_US\prefs
\Documents and Settings\<username>\My Documents\maya\2011-x64\en_US\prefs
You can change the location of your preferences and other important Maya folders (projects, etc.) by using environment variables. See File path variables for more information.
Most preferences are saved as text files of MEL commands.
For descriptions of the options in the Maya Preferences window, see Preferences overview.