I tend to use the high altitude f/p when I'm doing an IFR flight. I know the built-in flight planner isn't that great... but its free. This tends to somewhat mirror r/w flight plans. When I'm doing VFR I usually use the VOR-VOR or the direct option to use as a guide when I'm hand flying the flight. When I'm doing transatlantic flights or transpacific flights I'll use the free version of routefinder and then compile the route with fsroute. Fsroute will let you save it in whatever format you want.
Free version of Routefinder:
http://rfinder.asalink.net/free/
Fsroute:
http://www.fsroute.com/