Two important types of rooms I see as being inevitable would be storerooms and vaults. Especially now that nobles might have some use, there's a lot of cool ways these could be handled.
Storerooms would be a room that functions like a stockpile, only assigned like a room, from containers (shelves or chests). These could store anything from general goods, to trinkets or tools. These could be owned by a dwarf- a store owning dwarf could keep extra merchandise in a storeroom. They could synch up with workshops or stores, and store tools or materials associated with them. They could have a special menu, like stockpiles have- but the big thing is that they could either be useable by everyone or only to certain skilled crafters or whatever. They'd be more 'long term' than normal stockpiles, and would function as nice focal points for economical dealings, along with stores. Bookkeepers could hang out around them and inspect them, or
Vaults would be rooms, owned by a noble or other rich person, or the fort as a whole, which would store precious metals, coins, gems, and trinkets. They could act as a treasury, or just a place for rich dwarves to keep their glittering goodies. Naturally, these would be big targets for intruders of all sorts; and reinforcing the walls and posting guards would be great fun. There could be loot in containers, or just overflowing onto the floor. These could be assigned from maybe a normal door, or a specially made 'Vault Door' or something.
The important thing for both of these is that they be intuitive to use, and worthwhile to create. Having a set place for goodies, where accountant nobles can tabulate is good. Likewise, having a safe place for your fort's precious gold is nice too.
I'd like to hear what others think (This was written rather quick)- about these two rooms and other similar things that could be added in eventually to help organize and protect loot.