A techy point of view:
While flash is a very attractive format to use, it isn’t as widely accepted as Macromedia would lead on.
Not everyone has the plugin that is required to view Flash files and it usually doesn’t load nearly as fast as other formats. By the time a page loads your banner, the visitor has navigated his or her way off of the page.
Just to throw it out there: never use flash for navigation. Even if the user has the lugin installed, Search Engines don’t think highly of flash files.
I’m not sure what the click through rates are for flash versus animated gifs, but I’d personally be more likely to click through on a gif as opposed to a flash.