I just got a tip from the Profession forums the other day indicating that gem stacking is working on the Test Realm. I logged in to check it out and sure enough! Gems are now stacking properly when you cut them :) I tried this on a couple of different cuts I had and made sure there was no room in my bags for gems to hide. It looks like one of our most popular Pandaria wishes has already come true!
I should test Alchemy as well, shouldn't I?
aaaannnd Living Elements still not stacking. I had a stack of Fire in my bag, did the transmute which made 14 Fire and proc'd 12 more fire. Each in a separate stack. Oh well.