Woo Hoo - Cut gems now stack. With this I will be holding more per cut of each gem.
But not during crafting. Bother. During crafting, you still use one slot per gem. My guess is that this will be fixed by Blizzard "soon"; for an arbitrary definition of soon.
There is an addon I use to help with stacking and sorting - genie, and it works well with crafting bags.
/genie bag work (to sort & stack your bag)
/genie bank work (to sort & stack your bank)
and for GM's, you can sort & stack a guild bank tab by clicking on the genie icon on your minimap.
I am not naturally the 'tidiest' crafter, but genie allows me to fake it.