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In early 1999 when I just began with my sites, I used two submission sites.
Most were very minor SE's. The result for me from the majority of the submissions was unwanted spam.
Methods have changed drastically for submssions in the past four years. Some require payment.
I would suggest reading the MANUAL submission instructions on the major SE's and tailoring your pages to gather their cooperation BEFORE submitting. It the end it will prove most beneficial to both you and your site(s.)
the tool spiders your site, and provides advice based on what it finds. it looks for url probs, spam issues, and optimization issues.
after that, if you choose *you* can submit it right from the site. it includes Inktomi paid inclusion.
it also has a keyword research tool that provides data from MSN.