Though frequently neglected in developemnt world, well organized XHTML code is a prerequisite for a Website doing well on SEO aspects.
Not once we have been working on Websites whose construction required top-class CSS, in order to achieve identical display / behaviour in all major browser.
JavaScript solutions we implement are in accordance to world standards (we mostly work with Mootols, but we also have experience with JQuery and Prototype), but quite often we need to prepare our own, custom JS (or Ajax) code. Whatever way we choose, we will keep HTML, CSS and JS apart, in order to ensure ease of maintenance.