Gebabbel is a GUI for the famous gpsbabel, a command line tool to convert various GPS file formats back and forth. Thanks to gpsbabel, you cannot only convert files but also exchange data with your GPS device (e.g. Garmin and Magellan) directly.
KMLTool (better name wanted) is a command line tool written in java, mainly designed to automate the process of converting kismets .gpsxml/.netxml files into google earth's KML files, with some features i used to miss in other programs for this job.
Wayconv is a simple command line tool for converting between different GPS waypoint (named position) formats. The program is written in C++ using new style iostreams/std, and is portable to Windows and Unix platforms.