have Both of these and Model-2-Sprite worked best for me, What i did was load the 3D Model, then extracted the Views/Animations i wanted and saved them as TGA then used Paint.Net which is free to remove the background colour, Just use Magic Wand. Then save as PNG, the whole thing takes about 2 mins.
Yes, if you only use downloaded ready to use 3d models, or you have no idea how to use 3d applicaions You could do what tonycrew said.
I'm using 3ds max, and it can all be done at once with it - and any other 3d application - models, animations, save png's with transparency :)