The common downloads from SS's site are: Windows, OSX, Debian/Ubu, RH/Fedora, standalone Jetty, and WAR.
Do I assume correctly you're referring to the WAR version that gets run in a java servlet container such as Tomcat? If so, the process is pretty simple:
1. Stop Tomcat.
2. Delete $TOMCAT_HOME/work/Catalina directory
3. Delete (or move someplace) the $TOMCAT_HOME/webapps/subsonic directory
4. Move your new version's .WAR file into $TOMCAT_HOME/webapps
5. Start Tomcat, which will automatically unpack all the files stored in the WAR archive, creating the new "subsonic" directory under webapps.
That's all you should need to do -- your database info (reviews, ratings, users, etc.) will be intact because those are located elsewhere at /var/subsonic.
Bear in mind that any personal modifications/changes/hacks that you made to any of the JSP files in the old version will need to be re-done on the new version's files.
If you're running Windows, then the above should be used as a guide, substituting windows-specific directories/locations etc. where necessary.
If you're truly using java source code and compiling all those class files yourself from scratch, and not using Tomcat.... then ignore the above
HTH,
Supra92