This is really pretty straight forward though finding the links in a site or page certainly may not be.

Some javascripts and DHTML make these links hidden from search spiders which cost your site with regard to page ranking. If the spider cannot seem them they do not know they are there. Some navigation layouts are your enemy. Some are really search engine friendly it is your developers job to use a navigation tool set that is not only pleasing to the eye but friendly to the search engines as well.