I set my pop cap to 500 so I've been experimenting with various large fort designs. (I have yet to hit 500 so far though)
Everything is based off a central 3x3 staircase. The only design constant I've kept is my bedroom designs. All commoner rooms are 3x3 with a bed, 1 chest and 1 cabinet. Rooms are kept 100 to a floor in a 50/50 efficient/inefficient design:
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My initial dwarfs get 5x5 rooms with attached 3x3 office and a communal (for them) private dining room.
'Good' Nobles gets 7x7 rooms with attached office and private dining.
'Annoying' Nobles get locked naked in a 1x1 room with an upright (training)spear trap for 5 minutes with the lever on repeat.
This usually settles then down for a season or two, but eventually then end up in the next level...
'Bad' Nobles get dropped into my naked goblin pit to be beat on until they either die by goblin, or goes berserk and kills them all. Berserker nobles are then returned to 'good' status and allowed to rejoin the fort.
Beyond that I tend to use large open spaces to house stockpiles and workshop areas. I'm not a fan of small closed off general areas.