The use of plug-in objects and script can look fantastic on your web page, though an excessive use of those objects will often blind a search engine spider. This in turn will lower your chances of being indexed by the engines. This practice is usually seen as the most common reason why your pages may not be indexed. If your web page URLs are embedded in JavaScript, most of the search engines can not see them and will not index these pages at all, the same applies to FLASH and other objects, while a search engine can not see an image, it cal always see where the image is linking and with the help of (Alternative text) know what the link says, FLASH objects are not the same, the search engine can not see links from within a flash object and most search engines do not parse java script.

If they are a must (for example your website is all about flash) you should have a footer with the links repeated at the bottom of the page.

Try to keep your page simple when it comes to HTML, and try and use more tables and less images, and use (search engine hidden objects) only where necessary. Constructing an entire page from JavaScript can make your page almost blank to most search engines.