My business mileage application serialises a variety of data (eg journeys entered, known journey distances etc) to XML which I wanted to store in a sensible location. To keep things nice and simple, I chose to store the XML files in the same location as the install. That way, I can easily find the files and, should I wish to clear any remnants of the app from my device I just need to delete the folder.
The challenge was to use reflection to find the application path. How to do it can be found on the Compact Framework FAQ at the OpenNETCF wiki.