I have found that with JRun I can put property files in the servers\default directory and can access them with no path information, but just the name of the file:
String propertyFile = "project.properties";
props = new Properties();
try {
FileInputStream fin = new FileInputStream(propertyFile);
props.load(fin);
fin.close();
} catch (Exception e) {}
That may not be a great place to keep property files, but it seems to work