Using the Professional version of Banner Effect, you can create animated GIF banners.
Use the File/Create an animated GIF banner... menu to start the creation. A window will appear asking you how many frames per second are required for the GIF animation.
Choose a value between 5 and 10 frames per second, and do not hesitate to run tests with several value until you have the quality and size requirements.
Then a gray window will appear showing the progress of the generation. Once the build is complete, the program will ask for a filename to save the GIF banner on the local disk.
You should know that animated GIF usually takes more space than its equivalent in Flash or HTML5.