Pages that include these types of scripts make it difficult, if not impossible for a search engine spider to read the page content or follow any page links. As search engines need to find internal links to navigate your whole site, scripting can cause parts of your website to go un-noticed.
Search BoxesAnother issue is 'Search Boxes'. In the site design, make sure all your pages are available to be navigated to using a menu and footer links and don't rely on just the Search Box. Spiders can't use the Search Box so again, your website is going to loose out on potentially important page rankings. The same goes for sites that have content behind a secure zone or 'submit' for of some sort, as the spider can't click 'submit', the content will go un-ranked.
Flash / SilverlightA fantastic application for videos, slideshows and interactive presentations for your site BUT the search engine spiders cannot see what content it renders. Remembers the Googlebot is not human so although your site may look fantastic, it does not show any search engine content so will be heavily penalised for it. Although some bots can see what's in a flash object, it is still not clear cut how much or little can be read. The other big issue is that Flash is not able to be viewed on iPads and iPhones. This looses a huge market that is steadily growing and gaining more search power.
You don't want to be in a position to bandaid your website in fear of it ranking badly. Ensure you setup your site correctly the first time to get the most benefit out of it.