I don't see a reason for a directory of most used blocks, unless you are using a graphical interface to scroll through an endless list of blocks. I would have thought that you would remember the names of the most used blocks and would just insert them by name from the command line: bada-boom.
As for the other issue, be aware that the current dimstyle, textstyle, and layer in the drawing where the block was made will all come along for the ride. I wish someone had told me this when I started. You need to be quite deliberate about the way you make your blocks or you will lose control of your drawings to some extent. For some this of no concern, for others a festering sore.
Blocks that are meant to be inserted on different layers should probably have their entities on layer 0. Blocks that are always supposed to look the same no matter what layer they are on should probably avoid using BYLAYER or BYBLOCK linetype and/or color. Blocks with entities that you might want to vary in appearance yet keep on the same layer should probably use some BYBLOCK linetype and/or color.