1. Avoid flash and frames
Flash content is completely unreadable to search engines, and frames are not normally crawled by them either. It's OK to have smaller embedded Flash elements within an HTML website but an entirely Flash site will need a separate HTML version. Individual frame pages that do get picked up by search engines tend to get isolated from the site navigation, leaving them out of context.

2. Don't hide text within graphics
Text in graphics can't be seen by search engines so it won't be matched against the phrases people are searching for. Nowadays, style sheets allow a good range of text formatting so you don't have to completely sacrifice on style. If graphics are essential, use ALT tags to provide appropriate descriptive text.

3. Divide and conquer!
Pages dedicated to separate distinct topics or items get a stronger match on search engines than pages that try to cover everything. Try to divide sites up into separate pages (e.g. a different page for each subject, category, product, news item, etc).

4. Put keywords in link text
The text in a hyperlink helps tell search engines what the target page is about. When you link to a page try to use HTML text (as per point 2 above) and put some relevant keywords in the link text. This is especially important for your navigation menus.

5. Place popular search terms in the page text
Try to make sure the visible text on the pages contains the words and phrases that potential visitors are actually searching for. Don't duplicate phrases unnecessarily, and try to keep it all relevant to the specific subject of that page.

6. Good title tags
The <TITLE> tag is usually what the search engine will display as the link text in their search results - you have around six words to clearly state what the page is about.