The following is what I've suggested to J&L some time ago, to reduce a lot of clicking:
1) You left-click an item so that it sticks to your mouse (like usual).
2) You scroll up on your mouse-wheel, unloading the inventory (that you took the item from) of equal items, one after the other, and adds them to your mouse.
(The number of items are indicated at the held item and scrolling down puts them back in the inventory they came from.)
3 a) You left-click in an inventory (or the ground) and as many items as fit in the new inventory are moved there, leaving the rest on the mouse.
3 b) You right-click on a kiln or something (while holding fuel) and it refuels with as much as it can.
3 c) You right-click on the ground (while holding seeds) and it plants one seed.
Simple, fast and only 2 clicks (except for seed-planting, and a little scrolling). :)
Shift-clicking would still be left as is, 'cause it has its own uses, but i prefer this method over any modifier keys since the mouse is the main tool
for playing the game, and I want to be able to hold the mouse in my right hand and my...teacup in my left as much as I can. :)