Do not use JavaScript menus. Search site crawlers aren’t able to read JavaScript, so you’ll be losing any potential benefits of cross linking pages. Remember related keywords. Using your most important keywords is not enough. You also need to use words that are related to your required keywords. They are searching for relevance. By using related keywords you help the search website know what your site is about.
Forget Flash. The problem with a Flash-only website is that there is nothing for the search sites to see. If you would still like to use Flash, be certain to include an HTML version of your website so the crawlers can get the required info from your site. This could be aesthetic, but it’s's as good as being blank to the search sites. One way around this is to use ALT-text (regard it as an unseen label for text that crawlers can see) that contains the same words as your strap line. Bonus tip: use keyword heavy ALT-text for all the pictures on your website.
Being conscious of these few things will aid in keeping you from being unintentionally penalised for your SEO attempts by the search websites.