Link Structure
The first step to optimizing your website internal structure in ensuring your website is easily to navigate. This is of benefit to your users and search engine placement. If the search engine's web crawler can't find your content then it can't be searched for. Important sections should be one click away from where most of your users enter your website. If you don't have a site map you should make one and make sure it is accessible from every page. This will ensure search engines can quickly find every file on your web site. Google recommends that the site map be split into pages with less than 100 links.
To check if your website has been fully indexed enter the 'site:www.domain.com' command into the search box. This works on Google, MSN and Yahoo. If you find missing pages and your site has been indexed for a while then you should check how you link to the page internally. Search engine spiders don't follow links in Javascript and Flash so you must provide a text link in HTML to pages for spiders to follow.
Validating Your Links
Using a program to validate that any your links aren't broken will help ensure a high quality user experience and make the web spider's job easier. An excellent tool for accomplishing this is the W3C Link Checker.
Keyword Rich URLs
Yahoo, in particular, but all search engines place importance that the search terms are in the URL. A good url should say what's on the page without being too long.
Bad Example: http://www.foobar.com/things/history.html
Corrected: http://www.foobarjapan.com/hiroshima/history.html or http://www.foobarjapan.com/hiroshima_history.html
The corrected example will place much higher in search engine results for searches containing the keywords: Japan, Hiroshima and History.