here's a link to a list of free seo-friendly directories that you can submit to - manually i'm afraid. http://info.vilesilencer.com i found this site from the webmaster-talk forum.
The best way to submit to search engines or especially directories is to submit "manually". Check out http://www.google.com/addurl.html http://submit.search.yahoo.com/ http://beta.search.msn.com/docs/submit.aspx?FORM=WSDD2 Good luck...
Get links is the way to go. The only reason i see is sometimes to refresh info with yahoo for example, i noticed that it's working when they can't let appear actual info. Google for example is known to prefer finding sites by itself, i never submitted any site to GG and lots of them are doing well on broad range of industries...even though it takes time on competitive markets. Of course is the point is just to index a site without more expectations you still can submit, that's fine. I find submit-it being a good service for what it is despites what other SEO may say.
Be sure to give them an email address you don't plan to use anymore though - those free submit programs are the BEST way to get listed in every spammer's database on the net. I don't actually think you should waste your time. The only search engines that really matter are Googe, Yahoo and MSN and an automated submit won't really help you much in any of them. Focus on trying to get some decent links to your site instead.
I'll just chime in here and re-itterate what's been said. Don't even bother with submitting to the SE's. Get yourself some good incomming links and you'll be indexed fairly quickly. Inbound links are the key to getting your site found and high in the SE's.
That's a great little list. I have used it myself ..... some really good, free, spiderable directories in there. Just a tip .... there are heaps of sites in there, so if you're not really patient, do this: Start submitting to the PR6 and higher sites, then submit to all the PR5 sites and so on, 'cos there are quite a few in there and you might as well start with the best. Have fun!
I use freewebsubmission.com to submit my new sites and look for backlinks afterwards. I wont hurt you its FREE
I'd suggest submitting at less known sites, the big ones will find you. Search Google for "submit url" "submit site" and choose whatever site you like. Also, the big SE will only find you if you have some back links If you don't, then submit manually.