Stefan and Milton
Those are good ideas but they work only if you are restoring to the same hardware with the same other software installed.
If you intend to save FS to an external drive to move it to a new pc in the event of a total failure and complete system rebuild with all new hardware you need to do it more piece meal.
Back up the FS9 folder (copy to the external drive)
Back up the Applications data folder for FS9
In XP C:\Documents and Settings\{your user name}\Application Data\Microsoft\FS9
In W7/Vista C:\users\{your user name}\AppData\Roaming\Microsoft\FS9
The two basic registry locations you will want to export are
Key Name: HKEY_CURRENT_USER\Software\Microsoft\Microsoft Games\Flight Simulator\9.0
Key Name: HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Microsoft Games\Flight Simulator\9.0Key Name: HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Microsoft Games\Flight Simulator\9.0
If you don't know how to work in the registry read up on it before you go into it. A simple mistake here in the wrong place can render your PC unbootable.
This will not work for some of the more technical payware that needs to see its registry entries to work. Those you will need to do a reinstall on.
Remember when if you back up these registry locations when you restore them on the new PC you must make sure that the FS folder is in the same path or some of the registry entries will be broken.