When a search engine crawls your website, it does not appear how it does to me and you. The spiders that are sent out to crawl your site can only interpret certain things and that is why it is important to build a website that is designed with SEO in mind. An example of this is an image that contains text within it, the search engines will not be able to read the text within the image but it can understand what the image is a bout from the file name, alt tags and image titles.
You need to ensure that your most important information on your site is in HTML format as Java applets, Flash files, images and other non-text content are often ignored or devalued by search engine spiders, despite the advances in crawling technology.
Having a crawable navigation to your site is crucial. Many companies make the mistake of not having a search engine friendly navigation thus meaning many of their pages do not get crawled and therefore do not show up in the search engines results pages.