According to a pixel artist friend of mine, all the companies he's worked for using those types of anims will build a proprietary tool that essentially works like Flash in a pure-bitmap context; tweening, scaling, rotation, and bitmap cutouts(e.g. parts that bulge and bounce, like the belly of a fat character, simply reuse an area of the sprite and layer it on top). These tools are used for menu layouts and level design as well as sprites.