There's some pretty good evidence that suggest if your keywords aren't near the top of your page they won't be ranked as highly. There's also evidence which suggests search engines don't look much past the first 25k or so of an HTML document, or it is weighted correspondingly lower if they do.

So if you have some funky JavaScript that controls all your mouseovers, scrolls text across the page, serves up the current date, time and second, and implements mouse trails, chances are you've used up pretty much all of that first 25k with useless text, while burying your keyword-rich content at the bottom of the page where it gets ignored by search engines.

Fortunately, the solution to the problem is a simple one. If you use JavaScript, put all your functions in an external .js file and link to it in the header tag. This will not only help to improve your site's search engine positioning, but it will also ensure your pages load much faster.