Ever since the Buffalo PIREPs stopped storing the exact flight path anymore (only a straight line between departure and arrival airport) I've been looking for some alternative tracking software, and I think I've finally found it.
It's called FS-Duenna, and was originally written to track round-the-world races (some of the online flyers here might already be familiar with it): http://johannesmueller.com/fs/web/duenna/
It's free, and it stores your flight path as well as some other relevant statistics for the whole flight (like altitude, wind speed, etc). The data can either be called up online (for sharing or verification), or downloaded for offline reference.
For example, here is my latest flight on the DC3 world tour: http://fs-duenna.com/flights/ShowFli...ox8It6HoMkyiPE

The data can even be downloaded in KML format, and then overlaid on top of your original flight plan (in Plan-G, for example), to see how well the execution matched the plan:

(As you can see, I drifted off quite a bit on the long leg, due to some heavy western winds.)

Or, you can open the KML file in Google Earth, and actually see the whole thing in 3D:


NOW — since I seem to be starting more and more software whenever I do a flight (weather engine, WideClient, Plan-G, checklist in browser, and now Duenna), I've written a little utility that does that automatically.
And because I keep forgetting my password it also automatically logs into the BFLAcars client, and then it starts the list of applications. (Why is BFLAcars password protected anyway? Are people afraid that somebody could sneak onto your computer and log some "unauthorized" flight? That would be fine with me, actually...)
Once you're done with the flight, and close BFLAcars, it will then also close all the applications that were opened upon initialization.
The first time you run the utility it will ask you for your credentials and the list of apps to be started, and on subsequent runs it will do everything automatically.

The utility can be downloaded from here: http://www.kronzky.info/fs/BFLAcarsStarter.zip