Most of Rhino's settings are not stored in external files, but in the registry. Because there is not one single file that contains all options and personalizations, you will have to do a bit of work to transfer all of your custom settings. There do exist some shortcuts:
The easiest way to transfer the bulk of your settings is to use the Rhino command OptionsExport (V5), which creates a single file with MOST of the user customizations. Importing this file into another installation via the command OptionsImport (V5) will transfer the settings to the new install. You have a choice of which settings you would like to import, it is not necessary to import them all.
In V4, these two commands were named ExportOptions and ImportOptions, but were renamed in V5 to avoid confusion with other file import/export settings. Display modes are not included in the ExportOptions in V4, you need to export them separately! You do this from Options > Appearance > Advanced Settings. In V5, they are included, but you can only import then all at once. If you want to just transfer individual display modes, use the Export/Import buttons in Options>View>Display Modes instead.
The workspace file (.tb for V4, .rui for V5) contains all the toolbar info, one can copy this between installations as well. Unfortunately, this file does not contain the on-screen locations for the toolbars, only the toolbars themselves and whether they are open or not. As you can also customize menus in V5, the .rui file file also contains menu information.
Other things that might have been modified could be your template files, display modes, installed plug-ins, etc.
For V5, your toolbar file is located here:
This is a hidden folder in most Windows installs, the easiest way to get there is to type %appdata% in the search box.
For V4, your toolbar file is located here in Vista, Win 7 or 8:
This is also a hidden folder, type %programdata% in the search box as above.
In XP, it should be here:
C:\Documents and Settings\All Users\Application Data\McNeel\Rhinoceros\4.0 or 5.0
A general transfer procedure might look like this:
OptionsExport (V5) or ExportOptions (V4) - creates an .ini file
OptionsImport (V5) or ImportOptions (V4) and import the .ini file created above