As of December 26, 2007, JFlagCap Version 1.3 is available for download from SourceForge.
There are two files rather than three this time-- one for Windows users and one for everybody else (which works on Windows too). The Windows .exe is a setup that contains both JFlagCap and the Java 1.6 runtime so that it doesn't need to be installed separately. The .tgz contains JFlagCap and nothing else, so Java will need to be installed already before running JFlagCap.jar.
The game and this website are both made by Mark Burger (currently seeking employment.) Feel free to contact either me or the jFlagCap forum if you have any questions or comments. If you prefer chat, I am on ICQ at 119420913.