This would be nice... I just bought a room to stuff the things in, not knowing the limits on stored containers and item counts. Now, it seems I must purchase many bags to store it all in, or else deal with a lot of inventory clutter.
I once played an Underdark PC who kept 2-3 bags full of reagents on him all the time. Not a problem. Only harvest stuff you will use, and just use it up making things. Lots of the products stack.
I'd like to point out this isn't likely to happen, mainly because it would require a re-work to the crafting systems to take into account stacked ingredients properly.
Yeah. Just make stuff with it. If you don't know what to make with a reagent.... well then don't pick it up. Or keep limited quantities.
The items can't just be made to stack, however. The icons chosen for them simply don't have the capability of stacking.
And as Box has pointed out, using stacked reagents doesn't work with the current crafting system. The items must be separated out into individual items before you can actually craft with them.
Also, that stacking and non-stacking is hardcoded. Misc items, small, medium, large, and thin do not stack.