I do not know any standards for skins.
In any case I prefer a)

Thanks Slamp
It pays to establish a method as files like Forms, Comments etc etc really do need CSS/Images etc per skin

My personal practice is like this: (b2evo skins or any sites)

/rsc/styles/sheet.css
/rsc/img/picture.png
/rsc/js/javascript.js
/rsc/swf/shockwaveflash.swf
/rsc/vid/videofiles like .flv .div .xvid .mov etc.

Anything that is a "resource" I put it in /rsc/*subgroup/

Then anything of "includes" under /inc/*subfolder/

It also makes it easy for those who will edit the skin, and at the same time, in a way influence them to follow some standard or organization of files.

And it's easier that way, you know where to look.