I believe Fort Emergence has a room that actually is labeled "storage." You could leave items you want to keep anywhere, but it does work best to drop it on the floor of a space that you will remember to check later.

There are three spots that are specifically set up for parties to leave extra gear and treasure; --the storage room in Fort Emergence (an NPC tells you that you can leave things there when you ask about getting supplies)
--the manor house that is for sale in one of the towns (I believe its the town under siege by giants?) You have to buy the place, but when you have you get access to a whole building where you can establish your party
--the abandoned farmhouse in the mountains in central Valorim. I can't recall the exact location but it's clearly laid out as a base for players to leave their stuff and rest. That one is my favorite because you can sort of decorate it and you have separate cabinets and chests for food, crafting supplies, gear etc.

Don't the Avernum games save every item dropped in every static location?