Many types of software are used in animated commercials. 3D commercials these days often use Maya. 2D commercials do use Flash sometimes or ToonBoom etc. Along with a whole mess of graphics software, video editing tools and special effects plugins. I work for a company that does Animated TV Commercials and we use all of these as well as Final Cut, of course Photoshop, and lots of plugins. Flash is still a very useful tool!