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There are, of course, solutions to this that will appease both
website designer and search engine optimizer. As a suggestion, consider using standard rollovers and/or CSS formatting to develop a graphically pleasing navigation menu. Unlike most JavaScript menus, neither standard rollovers nor CSS will "hide" your website's links, allowing search engines to freely crawl and index your websites pages.
If a JavaScript navigation menu is truly needed to attain
desired look and feel of your website, than consider adding text-based links elsewhere on your website's pages, such as
bottom. Bottom navigation schemes consisting of text-based links are becoming very common now-a-days, as they ultimately provide your website's visitors, and search engines, with another source for navigating. Another suggestion would be to develop and allow access to a sitemap containing all of your website's pages.
Flash vs. HTML - Flash is a pain in
sides of all SEO consultants... but it doesn't have to be. It is possible to mix Flash with HTML to create a search engine friendly website that still allows for a rich media experience.
My suggestion for when developing a website using Flash is to create separate pages, those in Flash and
others in HTML. Not only will you be giving your website's visitors a choice of which version he or she would like to view (which most will appreciate), but you will also be giving your website
chance to be indexed and ranked through your HTML versions. A very good compromise if you ask me.
Dynamic Websites - Depending on how your particular system is configured and how your website's dynamic pages are created,
use of dynamic websites can either be a great thing or a very terrible thing. Because dynamic web pages are data-based driven and are created on
fly, they are usually assigned URLs containing very large and strange looking parameters. These parameters, amongst other reasons, are needed in order to sort products and generate a central navigation for your website's visitors. At
same time, these parameters make it very difficult for many search engines to crawl, follow, or index your website's pages.
My suggestion to this problem is to consult with your development team, and your search engine marketing consultant, and have them consider developing your content management system using either ASP (Active Server Pages) or CFM (Cold Fusion). Either one of these "dynamic scripting languages" has
possibility of converting
URL's query string from "?" (which will usually stop a search engine from indexing
page) into "/". This process, and a few others, maybe all that is needed in order to give your dynamically driven web pages
opportunity to be indexed.
In my experience, designers who understand these and other common search engine friendly design issues are perfectly capable of designing around them, without sacrificing their design or future search engine rankings. As long as
designer and search engine optimizer come together in
very beginning, as opposed to after
website has been created, than finding a compromising solution to each of their needs should not be a problem.

I am a search engine marketing consultant and I have been developing, maintaining, and successfully ranking websites since 2003.
I am primarily focused on not only helping others to develop their own search-marketing campaigns, but I’ve also been consulting and educating them along the way.