I\'ve got some elements that I\'m moving across the page very slowly. Essentially, I\'m decreasing the left margin of two images over a span of 40 seconds or so.
Vi
I just watched the performance of animation under Scriptaculous, and found similar CPU spikes: roughly 50% for IE, slightly better performance (16-30%) for Firefox -- both on a DuoCore PC. Since both JQuery and Scriptaculous work by changing the underlying CSS, I think it's safe to say that any Javascript implementation is going to be computationally expensive.
You may well be stuck going with Flash.