Have you tried http://directorysubmitter.imwishlist.com/download-free/ ? I used this a few years ago and I remember being able to add new directories and it keeps track of which ones you submitted to.

I have also looked into http://www.fastdirectorysubmitter.com/ but haven't had the time to try it.

I would agree that directory links are now of less value than before in terms of SEO. But if you still want to try to submit to directories, you can look at Digixmas- this software has a list of directories and I think you can also add yours to the list. This can be automated or semi-automated. Directories links still count as backlinks but most of these links are less of quality. I would suggest you focus more on building and marketing content and build backlinks to high pr and authority sites.