I am currently using digiXMAS SEO Tools. It's super fast and you have an option to use it for free (150 directories only though) or buy a list of directories from them.
I bought the $15 plan for one domain, which allows me to submit to over 1600 directories. It's semi-automated, but very convenient and fast. You need to download their submitter program first to use it.
I tried Easysubmit.com also. It's not as fast though but completely free. They only have about 500 directories now although they add more directories everyday to their list.