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This example by Dutch web developer Gaya Kessler features an impressive animation effect of cartoonish smoke emanating from factory smoke stacks. Kessler thoughtfully supplies a configurable jQuery plugin with instructions based on his site’s header, so that you may create a similar animation effect for your website. Live Demo: Smoke Effect
Sam Dunn of the web development duo, Build Internet, wrote a tutorial on how to create an animated landscape using transparent PNG images. The tutorial takes advantage of the popular jQuery Easing plugin to help with the animation and the 
The creators of the site youlove.us shares their code (and explanation) for making a seamless vertical scrolling CSS background; featured on the site’s header. The script is also dependent on the user’s system time; the animation starts at a different position depending on whether you visit the site at night or in the morning, a nice touch. Live Demo: youlove.us (web page header)
Glimmer, a JavaScript animation creation tool that leverages the jQuery library, has several live demonstrations for some of the things you can do with the app. For instance, with Glimmer, you can create cool animation sequences or make a spiffy and impressive rotating banner for your website. Live Demos: Freestyle Sample, Image Sequence Sample, Fade Text Sample
jQuery Blend is a plugin for animating CSS background images. The project emphasizes on web development best practices such as 

Editor’s note: As of April 16, 2012, this resource no longer exists so the link has been removed.
This animated tutorial goes over a similar concept to the youlove.us example of vertically moving a large CSS background image. Illustrations on how the technique works will help readers grok the concept more fully. Devirtuoso, the author of the tutorial, goes through due diligence by offering an IE6 hack for backwards compatibility.