You can copy the shortcut for ArcGIS Explorer and modify the target to look something like this:C:\Program Files (x86)\Explorer\bin\E3.exe" /AppConfig c:\path\to\appconfig.ncfg
This way, you can create an application specific shortcut. You would want to store the Application Configuration file in neutral location (non profile specific). Also note, the ncfg file doesn't have to be local, it could be a network location.You can also modify the registry so that the application configuration is automatically loaded for any user that logs in on the machine. The drawback being that it is difficult to load ArcGIS Explorer without an Application Configuration afterwords (barring another registry modification).More Information on Setting your Application ConfigurationIf you go the route of registry editing. You can create a .reg file that'll do the registry setting for you. The contents would like to similar to this: 32-BIT VERSIONWindows Registry Editor Version 5.00
[HKEY_LOCAL_MACHINE\SOFTWARE\ESRI\Explorer1750\Settings]
"AppConfig"="C:\\path\to\AppConfig.ncfg"
64-BIT VERSION
Windows Registry Editor Version 5.00
[HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\ESRI\Explorer1750\Settings]
"AppConfig"="C:\\path\to\AppConfig.ncfg"