As yet another example of avoiding what I should really be doing, a quick note about a reworked version of PygmyBrowse (see earlier posts here and here). Last September I put together a working demo written in PHP. I've now rewritten it entirely in Javascript, apart from PHP script that returns information about a node in a classification. For example, this link returns details about the Animalia in ITIS.
You can view the new version live. Going "view source" in your browser will show you the code. It's mostly a matter of Javacsript and CSS, with some AJAX thrown in (based on the article Dynamic HTML and XML: the XMLHttpRequest object on Apple's ADC web site).
One advantage of making it entirely in Javascript is that it can be easily integrated into web sites that don't use PHP. As an example, David Shorthouse has inserted a version into the species pages in The Neartic Spider database (for example, visit the page for Agelena labyrinthica and click on the little "Browse tree" link).
