Lets see...after reading all of these threads there are 2 camps.
Camp 1: We have a spell that turns you into most anything. Some of these creatures have limbs, some do not. Some have arms and legs, some do not. Lets apply common sennse and say that as a transformation-type spell that it really does not matter what you WERE, but what you BECOME. This rule covers all possible contingencies like missing arms. Hell, I could use a wish to get my arm back, but the same level Shapechange won't.....
Camp 2: Lets look at the original form (and the zillion types it could be) and apply it to some of the zillion forms I could turn into...and not others. I know I can turn into a plant, elemental and many other forms without arms...BUT hey, lets beat up the one-armed guy even further and tell him that 9th level spell will work SOME ON THE TIME for him and not others.