Manually submission is the best way also get very effective(quality) back links and increase your PR.
Submitting by tools is not wise, some time ur site may be listed in bad neighborhood. if u have a list of sites then good, many submission tools are available. I did not try any tool until now.. so m not recomending any tool.. bu its available online.. can get from Google search
Directory submission is something that you can find @ low cost something as low as $35 for 100 directories. And most of the time they are affective.
@ rena, a site might get backlisted depending on how you submit them. If you get your site to a SEO Pro they would do it the right way and it will take months to have your site submitted to hundred of sites.
I will recommend SENuke. It is the best search engine tools that can automate many of backlink building process. You can also automate link wheel using this tool which is the best method to dominate google. Other tool is Bookmarking Demon and it's great tools also. Also use Market Samurai for keywords research. Hope this is what you are looking for.