I always like to find a small hill, preferably next to a couple of other small hills, but not necessary.
At the south side of the hill I make my large entry hall, with 3 squares thick walls and 3 rows of floodgates. This entrance is ONLY used by wagons. On top of the hill, I remove all of the ramps and make a single retractable bridge to the north. (to another hill/a bigger mountain). Here is where I also build my siege engines later on.
On top of the hill, I usually build a big tower for the millitary, with barracks, weapons and armor stockpiles, archery ranges, sparring areas etc.
On top of the hill,I make usually 3x3 staircases down. On the first level underground (the large entry hall) I usually don't have anything, except for a couple of spare stockpiles and my trade depot. Another staircase down, and here we have the "temporary living area". Here I make my stockpiles for almost everything, with corresponding workshops right next to them. Later on, I use a side hall to make this 40x40 meeting hall/dining room/statue garden hybrid. One more staircase down. Here are the quarters for the normal dwarves. They all have 4x4 bedrooms, which I usually smoothen AND engrave, but usually I only smoothen them. I make a small hallway to the north here too, and make my jail there. Another staircase down is my labor area. Here is my labor area. All possible workshops are here (except siege workshop, that one is on top of the hill) with enormous stockpiles for everything. A final staircase down brings us to the noble quarters, with 40x40 bedroom/dining hall/offices for my first 7 dwarvs, and 5x5 size rooms for all other nobles.
Any questions?