Search Engine Friendly Web Design
If you read my article on How Search Engines Work, you will see that the search engine spiders find websites and web pages by following links on pages they have already crawled and indexed. Therefore if you want the spiders to easily find your pages you need to make sure the structure of your website is flat. You should be able to get to every page on your website using a maximum of 2 clicks from your home page although ideally there should be a direct HTML link from your home page to every page on your website.
It can be easy to be quite blind when it comes to your own website so get a friend (preferably not an internet whiz!!) to use your website and ask them which parts they found confusing or difficult to use. If you make sure that your website is easy for visitors to use you will essentially be keeping the search engines happy and the spiders will therefore be able to freely move around your website. Do remember if there any parts of the website you do not want indexed eg admin sections etc then make sure that your robots.txt file prevents spiders accessing those files.
Always have a sitemap and submit that sitemap to Google using Webmaster Tools each time you make changes to the number of pages.
Use of frames can mean that only the actual frame is indexed with the actual page content taking considerably longer to be indexed as they are less easily found. I would never recommend use of frames if you want your website indexed by the search engines.
Use of Flash without a full HTML equivalent can still cause indexing problems despite Google's announcement last year that it had collaborated with Adobe to ease indexing of Flash.
Another factor to consider is the number of links you have on a page. Ideally you want the spider to follow links to all other parts of your website so additional external links that take the number of links on your page to more than 100 may delay the spiders in finding all of your website.
If you use php then you may end up with multiple URLs pointing to the same page because of the use of parameters. You will know you have this problem if your URLs have ".php?id=" in them. Content Management Systems CMS can also result in different urls to the same page content. Unfortunately this can look to a search engine as if you have duplicate content and duplicate content will be penalised. In addition search engines will very often not follow complex URLs of this type. Multiple php generated URLs can be overcome by using the meta tag <link rel="canonical" href="http://www.etc.co.uk/pagename"/>. Multiple URLs produced by content management systems will need to be converted to SE friendly URLs by modifying your .htaccess file but the method will depend on your particular server and you should approach Support for your hosting company to see how the file should be modified.
Some design features, despite looking quite nice, can completely block the search engine spiders, eg pages only accessible via a login box or search box, pages on a dynamic drop down menu unless, of course, you have a full HTML link to each page. However as with Flash, my feeling is Why pay for web design twice over, ie a Flash/dynamic site PLUS an HTML alternative. Instead put your budget into an even better more functional website in the first place. SEO4all can provide you with further advice regarding any of these SEO matters.