FS2004 / FSCOF / FS2002 / FS2000 Courseplanner 4.0.1, stand alone flight planner. Complete with a color map to track all your moves in a separate window.

Can be used with or without Flight Simulator running, (totally independent of FS). Allows you to use all the planes in your hangar, control the weather and much more. Will fly the aircraft for you and even pause the game near the airport in case you fall asleep.

You can create /load a flight plan, an adventure or just to follow your progress. Can also print a simple map to help you. Comes complete with the default FS database with all the airports, VOR, ILS, and airways.

But of course you can build your own database. (This version has the hot fix for 3rd party aircraft).