Dear Vjeran, your own jobs should implement the Tool Interface and ToolRunner. This gives additional standard options on the command line.
Also have a look at class ProgramDriver as used here: https://svn.apache.org/repos/asf/hadoop/common/trunk/hadoop-mapreduce-project/hadoop-mapreduce-examples/src/main/java/org/apache/hadoop/examples/ExampleDriver.java which further simplifies executing your MR jobs. Best regards, Jens
