

Contrary to popular belief, submitting sites to search engines does not result in improved rankings. The major search engines are constantly looking for new sites and look for new domains and their content as soon as they are registered. They also follow links from sites currently indexed to find new content.
There are very few search engines, with the minor directories usually taking content from the major search engines.
Not all search engines will index new content. Many request firstly that you submit and then ask you to confirm your submission so as to minimise the number of automated submissions.
Read the submission pages for each search engine to see when you need to submit and when submission is not required.
If your niche market is served by trade related directories, you will usually need to submit your site to these directories. While many will be free, you are likely to be charged a small fee for inclusion in trade directories.
Until your website is complete, you should avoid submittion it to any search engines. Missing links and pages 'under construction' will not give you a well ranked site.
Many search engines have a maximum number of submissions per time period: again read the submission pages and do not exceed the maximum number of page submissions.
Putting a lot of effort into link building and obtaining reciprical links has less effect on rankings than the sellers of popular scripts that help with link building would have you believe.
A few, quality links from relevant pages on other sites DO have value. Do not confuse these quality links with a link spamming / link exchanges from a links page, which includes your link with many other links, most of which are not related to your business.
Cost of Site Submission
Most search engines and directories accept free submissions. Do not be fooled into paying a monthly fee to someone who does no more than use a script to submit your site to hundreds of directories every month.
This has two negative effects: it costs you money and can harm your site's rankings.