There are many ways to create navigation menus, and there are just as many wrong ways as right ways. When building your navigation you need to be sure the search engines are able to read and follow all your links. If there are no navigable links for the search engine to follow they’ll assume you have a one-page site and move on.
Menus created using flash and JavaScript can be problematic unless certain measures are employed to ensure spiderability. The best bet is to create all your navigation links using standard HTML, or at the very least have alternate HTML navigation available on every page. This will ensure the search engines have no problems indexing all of your content.
This post is part of a continuing series on the topic of:
Optimizing for Maximum Search Engine Performance
Sub-Topic: Search Friendly Elements.