I would avoid using any automated submission tools, as these mostly submit you to worthless Free-For-All link sites (often designed to harvest your own email address for sending you more spam) and other worthless directory sites.
Using such programs can even get your site into trouble with the major search engines, as most of them prohibit automated site submission.
I would likewise avoid any paid site submission services, as most of these are just paying some guy to press the "start" button on one of these automated programs. SEO is a hot area - as a result, there are many people who read some simple, but out-of-date SEO advice from a book or the Internet, and suddenly think that they know what they want to promote their site.
Back a long time ago (back in the stone age, before Google even existed), the only way a site even got listed at all in searches is if someone manually submitted it to the search engines.
Likewise, the very first search engines had trouble even figuring out what a web page was about, and used Keyword Meta Tags to allow a web designer to "clue in" the search engine as to the purpose of the page. All modern search engines now have automated robots (aka "spiders", such as Googlebot, MSNbot, and Yahoo's Slurp) which continuously scan the web for new web sites and pages, and update or add them to their indexes. While most search engines still have site submission pages for historical reasons, not only are they no longer necessary, but it can actually hurt your search engine rankings to submit your site in this manner.
One of the reasons is that PageRank, which is used by Google to judge how "important" your site is, is based on what sites link to yours. If you did manage to convince Google to list your site before it has found your site naturally (by finding a site linking to you), your PageRank is going to be nada, and your search engine rankings are going to suffer accordingly.
To get a new site listed in Google, all you need to do is to put a link to your site on any other site that is already in Google. That's it - Googlebot will find the link on that site, and follow it to your new site. Directories are another issue. But there are only a handful of generic directories (plus possibly a few industry-specific ones for your area) that are even worth submitting to (some of which now charge you for a listing).
The best way is to manually submit your site to a directory. Automated submission should be avoided - if a directory is worth listing in, it is worth you taking the time to do it right.
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