Two of the most popular ones would be http://www.download.com and http://www.tucows.com . below are some of the best Software Directory websites, you can make use off.
Since again, these links too, do not get counted amongst the most important of the backlinks you will be building, a good idea would be to automate this. The tool I recommend for this purpose is PadBot and it is priced at $30. This tool covers both the steps that go into getting software directory backlinks – i.e.
converting your content into an EXE file as well mass submission of the same to multiple software directories. Again, automation is self-explanatory. You can easily figure out how to use PadBot once you download it. The link: http://padbot.org/