I have been asked a few times about this(how to submit..). It's pretty easy to submit your programs to Softpedia all you have to do is fill the form fields and submit.
They have different pages to submit for different platforms such as Windows, Linux, Mac etc.
Submit Windows Softpedia
Submit Games and Tools
Submit Mac OS Software
Submit Linux Software
Submit Mobile App
NOTE : you can submit your java programs in any section except Mobile.
Make sure you go to the right page, if you have a PAD file for your software already just fill the PAD form fields and submit if not fill the regular submission forms and submit. Don't forget to give your regular email address they'll send you an email when your program has been published.