Automated OR Manual Submission to Directories

Sites can be submitted to directories in two ways - manually adding your site to individual directories one-by-one and second way is to use automated submission software to do the job. While it is true that automated submission will be able to submit your site details to thousands of directories in a very small time and also free, but the method suffers from the following disabilities.

Directories require the submitter to enter a few characters (Captcha) to identofy you as a genuine human being. This step is bound to be missed by the automated submission and hence your site will not be submitted to these directories.
Some directories also do not allow automated submissions because it has been seen that automated submission software sometimes dump spam onto these directories.
Even if your site manages to get submitted by the software, it may not be able to drill it down to the correct sub-category where your might attract maximum traffis - hence the whole exercise might be one in vain.

So in light of the above it is most advisable that manual submission is the way forward, but it being so much time consuming you would be better advised to out-source the submission process. There is also the question of expertise here, a person having good experience in the field might be able to submit your site to most popular categories and avoid dull ones, bringing good traffic in return.