I think flv would be the best choice because of its lite, especially the flv video has been accepted as the default online video format by many popular sites, such as Youtube.
So it will be much more convenient when you want to share your video with the world.
Now I'm using a program could be helpful for you, not only it can convert flash to various video formats, but also image, keeping the original effects. And free trial version is also OK.
This is the download page: http://www.swfkits.com/swf_to_video/
Hope it will help you!