Roomba. Your Guild bank restacker.
Basic operation:
Open your guildbank. When things are all loaded up, you'll get a couple of buttons on the bottom left. Run Roomba and Scan Bank. If there's nothing to stack, you'll only get Scan Bank (which you can use to recheck the bank for new things to stack)
You can set the hotkeys for the buttons as well.
This addon should ignore existing items in your inventory, and only restack guild bank items. If you exit out of the guild bank before the stacking is complete (the Run Roomba button disappears) you will retain whatever stacks of items you were in the process of stacking.
This addon will naturally only run when the Guild Bank is fully loaded.