When was the last time you used a directory, of any kind, for any reason? Most people use Google, Yahoo! or Bing, and few people use the limited number of legitimate directories still available.
The danger with directory submission software is that you do not know the websites you will be submitted to, or their quality, or if anybody actually uses them.
An overwhelming number of so-called directories fit into the definition of link farms. If your website is blindly submitted to thousands of them, chances are good that Google will penalize you.
What you can do is research the few directories that may be useful to people searching for your business specialty, and manually submit your URL to them. This is legitimate link building, and it will help you. You can not achieve the same kind of results by buying some over-priced software, closing your eyes and clicking a button.
Stay away from directory submission software.