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I think that generally it only has the effect of alerting them to potential spam (last I heard the percent of legit sites that submit was less than 5% of all sites submitting, so that made submissions lists good places for SE's to go spam hunting). But there's a lot of heresay in this biz, and I'm guessing that one round of submission to the SE's probably won't do too much harm.
I'd proceed business as usual from here. The best way for SE's to find you is for them to find you naturally, on their own. That means by crawling the Web, and that means that they must encounter quality links that point to your site.
Bottom line: Go get quality inbound links.
Free URI Submit
Google
[google.com...]
Yahoo!
[submit.search.yahoo.com...]
MSN
[search.msn.com...]
I can't really confirm that anything happens once you submit but, I'm one that likes to cover all bases on a small campaign where link development will take time. If there is a slim chance that one of the bots will come crawling in a more timely fashion by using the free submit forms, then why not use them? At least get the process of crawling started. Introduce yourself to the bots. ;)