The design and structure of your website is by far one of the biggest factors involved in search engine optimisation. If your website is optimised from the very beginning, the results can often be seen a lot more quickly than an un-optimised site that has been online for some time.
In this section we’ll discuss some of the factors involved in site design that can affect the results of an SEO campaign:
How NOT To Use Flash
To put it bluntly, flash cannot be read by search engines in any shape or form. For this reason you should not make an entirely flash-based website, no matter how smart it may look. If you do intend to make a flash based website, a fall-over HTML based website should also be made. This allows the search engines and visitors with older browsers or no flash support to view the content on your website and, where the search engines are concerned, index the content for search listings.

In addition to a HTML version of the site, a HTML sitemap can also help visitors and robots navigate the site more effectively.
Dismissing Frames
One of the biggest areas search engines don’t look at are any sites that use framesets or iframes as part of their design. A frame is a part of the page that loads in a separate webpage from the parent page. If your site uses a frame on its homepage, you’re effectively throwing away all of your efforts before the search engine robot has even set foot onto your site. Several of the major search engines don’t index framed sites very well - if at all. If your site uses any form of frames, you should redesign it to omit them from your layout.
Be Clever With JavaScript!
To a search engine, JavaScript is simply displayed as the unparsed code that they grab from the web server. Because search engine robots are not browsers they can’t render the JavaScript code to display, whatever its purpose may be for the website. For this reason, any content you want to index in search engines - or have the search engine robots follow - should not be written in JavaScript. This includes navigations. If you wanted to have drop-down menus but this uses JavaScript then don’t worry, there are plenty of pure CSS alternatives around the web to choose from!

Problems With Dynamic URLs
Dynamic URL’s as basically URLs that have been generated by a back-end script such as PHP, ASP or a language that accesses a database. Search engines can sometimes have a bad time indexing these URLs because of their structure.
An example of a dynamic URL is:
http://www.some-domain.com/products.php?prod=blue+chair+abc
Where possible, you should use what programmers call ‘friendly URLs’, which are friendly on the eye as they give a lot more information than the above URL would.
For example:
http://www.some-domain.com/product/blue_chair_abc
The Wonder Of Image Maps!
Image maps are a wonderful invention for websites. They allow you to have links on top of an image. They are useful in dozens of situations, but they should never be used as the only source of getting to pages on the website. Along with an image map, you should also have a standard text-based set of links to the same page, as search engines cannot index image map URLs properly in many cases.