Scripts are complex codings which difficult for some browsers and crawlers to read, Some tough javascripts are read only by advanced browsers, search engine crawlers are not advanced browsers some of the browsers that search engines use find difficult to index high graphics, So it is best to avoid too much javascript,

Prevent creating menus in javascript or in any scripting language, Create menus in simple html or other crawler understandable language, Javascript menus wont be crawled by search engines, Best is to avoid using clickable menus and other important inner page links in javascript,

if you cannot avoid using javascript menus just add the links to a sitemap and attach the sitemap to the homepage or any other important page,

Another good solution can be to add text based footer links to the pages. This will ensure good Navigation structure too.