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I'd like to learn more about the pro's and con's of each but I'm not even sure what questions I need to ask here.
Loading speed? Accessibility? Copy protection? Usable in banner rotators? What aspects should I be thinking about?
One specific question: if two banners had the same or very similar look and feel as perceived by users, would the differences in how they're coded have any SEO implications? Does one format please spiders better or worse than the other?
regarding accessibility and seo, i would say that if you use the <img> tag to display the animated gif you are limited to the alt= attribute for providing alternate/accessible on-page content.
you can use the longdesc= attribute to link to more descriptive content or use the <object> tag to display the gif and provide alternate content within.
however with the flash banner you could use swfobject or a similar technique to provide alternate content to a non-flash enabled user agent that includes strong semantics and can be designed to degrade well for various browsers.