Just thought of this.
Anyone ever play Evil Genius? In that game you had an "Alert Level". Red = all minions arm themselves nd attack on sight, Yellow = all minions arm and continue jobs, Green = Standard.
What about applying a system like this in Dwarf Mode? It could just be another option to set in the orders menu.
"Goblin Army on the horizon!!! Everyone inside!!"
Example:
Green - All Dwarves go about daily activities, Fortress Guards/Sheriff all patrol as normal. (Optional addendum: All squads except manually activated are standing down.)
Yellow - All "Store Item" and "Move Item" jobs are suspended. Workshops function as normal. Fortress Guards/Sheriff patrol bedrooms and meeting halls(Guard Civvies). All "No Job" dwarves stay in thier bedrooms or meeting halls. (Optional: All standing down squads activated.)
Red - All jobs suspended and ALL non-military personnel retire to meeting halls and bedrooms. Fortress Guards/Sheriff patrol/guard bedrooms and meeting halls.
My reasoning behind this is sieges and large scale attacks from anywhere. As they are now any long term siege can easily kill lots of civilian haulers trying to recover items from the battlefield. Alert levels would allow you to put your fortress on "Hold" until the immediate threat is gone.
Personally I'd be more inclined to commit large troop numbers to a lenghty defense if I'm not worried about losing civilians to stupidity in the process.
Now for the drawbacks..... No hauling means rotting food or items outside stockpiles. Umm...still thinking about other drawbacks 
Retro
Final Word: I'm assuming the Trans/Burrows Arc will cover some of these issues. But I'd like to see a blanket order set for combat situations.