Even though transparent blocks are now visible behind other transparent blocks in snapshot 13w41a (ice and portal blocks are no longer invisible when surrounded by water! Yes!), there is now a new bug ,or not really a bug but a texture issue, which can hopefully be fixed easily.
When placing Stained glass, any stained glass block, against another stained glass block, the textures on the side of the two blocks that meet vanish. Im not sure if that is supposed to happen, but that isnt the problem. But when placing any stained glass block against another transparent or non whole block, such as the original glass block or fence post, the texture on the face of the two blocks that meet up start conflicted/ Z-fighting (I think it is called).
I have some pictures below to show what I mean.
Problem still exist in 13w41b.