Not sure how I missed this for so long, but ClickToFlash is a Safari plugin that not only stops Flash from running automatically, but also has an option to pull down h.264 video from a few sites, instead of Flash video. This should mean much smoother playback and lower CPU usage, especially on HD videos. And since it's an actual plugin that registers as a swf player, instead of being a hack into Safari, it works fine on either 32 or 64 bit versions of the browser.

http://rentzsch.github.com/clicktoflash/