I just started doing that. I use Blender to animate vector/bitmap images, you import them as planes. Subdivide the plane several times for smoother deformations. If its composed of several parts, you connect them via skeleton you might have to space the parts out along the Z axis. You'll have to learn about key frame animations in blender, and export the resulting animation as pngs. You can bring the pngs together into a sprite sheet using graphics gale export options or image magick.
It sounds complicated but once you get the hang of it, it's a very efficient way to animate.
this talks about how to export with the correct settings:http://flarerpg.org/tutorials/isometric_tiles/
you'll also have to turn on shadeless, face textures, face textures alpha in the materials tab of the image plane, and pre multiply in the textures tab of the image plane.
here's a tutorial on keyframe animations:http://www.youtube.com/watch?v=CFFhgutjZQk
it covers building a skeleton, rigging it with automatic weights, and also goes into the animation dialogs but all you need to know is how to enter a keyframe along the timeline. pm me if you need more help.