Some Facts:

• Submitting to 1000's of "search engines" is not the way to get your website out there.
• Less than 100 websites receive 99% of the search traffic.
• The majority of you traffic will come from Google, Yahoo and MSN. The other thousands of search engines collect email addresses and will spam you.

A reason to consider 1000 search engines: Submitting to search engines will give you back links and having many back links gets you listed faster in Google, Yahoo and MSN, But don't expect any traffic from the 1000's. There are only about 300 search engines (not 1000's). The other 700 (or more) are FFA link pages or classified sites.

IMPORTANT:

• Create a new email address just for search engines submissions (you will get spam).
• Most of the free search engines will ask for a link exchange. This makes it time consuming.
• The majority of free search engines will not accept sites with just a sales letter. Consider creating a blog where you post articles and submit that url instead. Link the blog to your web site.
• Determine your optimal keywords. Spend time researching your keywords. Keyword analysis and search engine optimization of your pages is a must to achieve high search engine ranking.
• Spend time writing titles and descriptions for the web pages you'll submit. Make sure to include your keywords in both.

Information You'll Need:

• Site Title (4-5 words, the more unique, the better)
• Site URL
• Site Description (100-200 letters, about 150 letters is the best)
• Keywords (about 4 to 5 words)
• First Name
• Last Name
• Contact Email (create a junk email address such as yahoo or gmail)
• User Name and Password (on certain directories, you may need this to login to edit the link).
• Preferred Categories (depends on the link directory site and the actual categories submitted to may be different)

Do it yourself for free

Submit to this listing:

http://www.directorymaximizer.com/seo-friendly-directories.php

selfpromotion.com

selfpromotion provides expert information about search engines. It’s one of the most reliable sources of information about search engines. This is a good place to learn about search engines. Rather than use some shady companies that submit to 1000’s of worthless web sites, you can submit your site yourself to search engines and directories from this web site.

It’s free but it's time consuming to wade through the options and set up your search engine submission(s).

For a small donation (any amount), you'll get additional features, they'll keep your settings and information in their system and resubmit your site(s) monthly automatically.

engineseekers.com

A friend of mine has gotten good results from using this service.
$34.95 to submit your web site to 67 search engines.

articleware.com (paid service)

http://www.articleaware.com/LinkSubmission/Default.aspx
MANUAL submission $42 for 400 directories.
You can pay an additional $8.95/mo for them to submit to newly added sites (optional).
You can submit up to 5 profiles that they'll rotate. Each profile could include different URL, title and email.
No reciprocal links needed for this service.

Personally, I prefer this option because it's inexpensive and effective, with manual submission and there is no reciprocal link needed. This one can give you best results for the least amount of time and money.