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Search Engine Optimisation - Making Sure Your Site has the Correct Structure
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First of all, you must ensure that your site is search engine friendly to begin with! If your site uses frames, then search engines will have difficulty in indexing your pages. There are workarounds but these are unsatisfactory. In a word, do NOT use frames!!!! If your site is database-driven, there may be question marks appearing in the URL which search engines do not like. You may have to employ a technique known as "URL rewriting" to overcome this and deliver search engine friendly URLs. If your site uses Flash, search engines will not be able to index the content of your Flash pages.
You must also ensure that there is a set of text links to every page on your website, on, at the very minimum, your home page. When you submit your site to search engines you submit the domain name on its own, which means the search engine will go to your (site root) home page (this is why framed sites dont work - the "home" page of a framed site is actually a frameset and has no content). If you have a Flash home page, you MUST place a set of text links in the HTML page in which the Flash movie is embedded. Don't use invisible links - if you want to hide them from the user, simply place them discretely at the foot of the page in a fairly small font.
Ideally, there should be a full set of links on every page, (or on a sitemap page which must be linked to from the home page). This means regularly updating the menu, laborious if you don't use server side includes or a database-driven system for your menu. But be careful with the latter solution as database-driven sites must be built carefully as search engines may not index their pages if they are constructed in a certain way. Also, be careful about changing the file names or file extensions of your pages if they are already indexed in search engines. You can lose rankings quite easily this way. Search engines only "like" certain kinds of redirects (often called "301" redirects), and even here you still can lose what you have gained.
Search engines tend to have a bias towards large, well-established sites. Thus the principle of putting out lots of pages helps - it increases the size of your site. The more content there is the more there is for the search engines to index. But make sure it is high quality content, otherwise you are abusing the search engines. Good content is king!
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