In order to change the encoding of JDeveloper's console to UTF-8 (in order to properly view e.g. Greek characters instead of "???") you should add the following line in the jdk.conf (JDEV_HOME/jdeveloper/ide/bin) and restart JDeveloper:
AddVMOption -Dfile.encoding=UTF-8
If you are using log4j make sure that you properly configure the console logger with the below line:
log4j.appender.console.encoding=utf-8