I think, personally, that depositing gems should be available in the banks, just as depositing gold is. It would merely be a sub-division of the bank's options, just adding gems to it. Deposit Gems, Withdraw Gems, Withdraw All Gems, Deposit All Gems.
I am sure I, and many others have run into several events where they were knack-sacked and was very upset about losing 1-8 gems, or so. So how about we just deposit our gems with a nifty new feature? The trick to this, naturally, would be that if you don't withdraw your gems before killing Orochimaru you lose 1/3 of them, but just as before you keep all gems on hand if you kill Orochimaru.
9 gems in bank --> Kill Orochimaru --> lose 3 gems
Rough rounding could be anticipated, too, naturally.
55 gems in bank --> Kill Orochimaru --> lose 18 gems
Feedback? Comments? Flaws? Add-ons?