General instructions can be found in the FreeBSD Handbook, under Porting Applications.

For &java; ports, there are unofficial standards:

    1) If it's a library then jar files go into:
          /usr/local/share/java/classes/

    2) If it's a stand-alone application then jar files go into:
          /usr/local/share/java/<application-name>/
        and  scripts to run it go into:
          /usr/local/bin/

    3) Documentation goes into:
          /usr/local/share/doc/java/<application-name>/

The more ported applications we have, the better.