My long-time design is based around 13x13 blocks that enables combinations of shift-cursor ten-jumps within the walls for 11x11 mega-room, divided to 5(+wall+)5 halvings, 3(+wall+)3(+wall+)3 thirdings, two-wide quarterings (rare) or a set of six single-width areas. It could be twelve single-width tunnel-rooms, reaching half way in, or more typically 3x3 superarray of 3x3s or a 2x2 superarray of 5x5s.
The latter tends to be my workshop layout. A 3x3 workshop (typical for for all but kennels, siege workshop and depot, I think?) with a stockpile overlaid to the 5x5 boundary. (Or do that, for sixteen spaces, but selectively unpaint eight of them and repaint a new stockpile on the same plan to fill in the others again. This provides either an adjacent-input and an adjacent-output, closely tied to the workshop concerned, or even two different inputs where combination reagents are needed, to give visual availability to the respect in- and/or out-piles. I might put doors centrally in each wall (or even every other wall-tile) or leave them as doorways (or "columns with gaps", also a popular way to outline a temple, pseudo-aesthetically) or demolish the internal walls entirely (but leave them unstockpiled) just because I feel like it (and/or want the stone, e.g. in a marble-layer, or another significant rock-type needed for colour/magmasafeness/etc).
I would also tend to 'stripe' fields (11 1x11s, again for visual availability/state) or array full-sized stockpiles, chequerboard them (lay down a full-size one, pick off every other square, re-lay a second chequerboard across all those gaps, to create a 'mingled but not mixed' stockpile), stripes (as per fields, eleven 11x1s) or other variations to cater for my whim
(I don't know if Steam-version does the "doesn't re-lay a new stockpile over a previously used tile" thing, yet. I found it nice to take advantage of, until now, but maybe the revamp has more 'afterthought' painting options, as per zones.)
Between the 11x11s(+external walls, or at least corner-columns if I fully open access to the block), I set 3-wide corridors with the central tils reserved for ramps (usually walkable, perhaps minecarted if I'm doing them out there) which are set to provide a vertically-diagonal cross-level transition that might be used instead of (or as well as) the "grand stairwell" set into the various major corridor-junctions.
And I extend this pattern vertically as far as I can (without involving cavern-spaces, which I'd staircase only through non-cavern bits and restrict my rooms accordingly) from the magma-forge layer (with magmaducts, as possible, dug beneath to tap into the available source) all the way up to the subsurface farms. The surface would mirror the wall-edges with built walls and also have strategic ditches into at least one (possibly several) Zs of underground where the pattern allows (around the edges, through reserved blocks, leaving catacombed rock promentaries, usually, with 'outside' pastures abve for animals, orchards, sunken 'outside but subsoil' farm-plots etc). I will raise the walls and roof over (with bridges) to create flyer-proof 'enclosed' outdoor areas
Again, I don't know how much of this remains viable under Steam-era gameplay. But I designed my ramparts to be climber-proof before there was really any risk of climbers, so minor adjustments alone may make this still a viable (if overcomplex) strategy.
Layouts and placements... Surface, anything usefully/necessarily aboveground (existing orchardy/plantstiony for trees, hand stretches of grass for grazing, the Depot, etc; hives may be built in ods corners or to an adsthetic layout, if I'm capable of apiary), within walls, with drawbridges and normal (and/or vanishing) bridges over excavated moats and a few sally-ports set up for quick ingress/egress by military or stranded units. Perhaps some pillboxes (access only from the fortress below, strategic viewing or ranged attacking made possible as required. Sometimes a bellygunner pillbox (effectively) built down from some above-surface enclosed walkway between two walled bastions, or similar. Sometimes the pillbox has a sallyport (or a sallyport entry can act as a pillbox), with suitable precautions. Some form of 'airlock' systems, to isolate these areas from common incursions, tend to be built where their accessway meets "the fortress internals".
Z-1 (and Z-2, if I'm lucky) tends to have the farms. Underground ones and "roof dug off the top" sunken-surface ones (to get pure soils, where available, rather than blocking boulders), with stairwell access also to surface-but-enclosed places (paddocks/orchards/etc). All the same level(s, more or less), and most farm-relient workshops (F's W, looms, querns/millstones, presses, breweries, butchers, kitchens, etc) perhaps dotted around where geology makes a potentially plantable area into less useful area of non-soil or significant rock. Though directly under the Depot (and maybe for more Zs, directly under that) is the Trade Goods/Etc stockpile (stripey) that used to be the "get these things off the wagon" hurry-upperer and intermediary staging post for all things not immediately useful/storeable elsewhere. As trading deals are struck, it gets reconfigured to take (un-crated) those things that I know the traders will value, plus anything else I'm planning on going to trade, eventually. Or at least the most importantly accessible lot (as it empties, or is TSKed to be, I may change the designations again).
In the first (few?) rock-layers, the (non-metal, and otherwise non-specialist) workshops. I tend to put a Mason dedicated to marble in any actual marble-layer, and mechanics with the intent to ultimately create olivine levers within any olivine-rich spot (or adjacent), but for basic and immediate multiprpose manufacturing (or the ultimately unimportant "diorite mug factory" that's turning the unwanted surplus of diorite into potential trading wares, and might put a diorite-stockpile around the workshop, as described, but am content to let it "trickle up" from where it has been scattered around during a given room-expansion diggingbin such a layer. I'll also have the main (and first) dining area, and may or may not establish social-zones/etc (including a series of mini-temples, and possibly a library), or leave undug/predug spaces for them as I have the spare time, inclination or actual need for them. As well as 'border-stockpiles' for the workshops (logs for the carpenter, the initial choice of rock for the wall-block mason to start upon) I may designate as yet unnecessary rooms (but dug out more for the purposes of making rock blocks) as secondary-staging stockpiles. As yet unneeded seeds, where the initial anvil gets put before I use it, a place to quickly draw down the logs created by felling those trees currently growing where I plan to dig out my moat/place my aboveground structures, picked plants (similarly in the way, but more picked for stocking than felled to prevent cave-ins), anything (except ores) that I haven't yet a good balance of storage/usage dedicated to.
Bedrooms I tend to put around the central core (or crossroads, or planwise around the depot-centred block, however the stairwell access leads) in the layers between the first and second caverns. I usually generate worlds with 10z gaps between caverns to give me plenty of uninterupted rock (and, if I'm lucky, plenty of types of rock) without having to worry about caverns except where my stairways punch through/around them. If I find some nice marble layers/patches, I'll tend to plan the fancier rooms there. Generic fancy, though I can choose another 'prestige' type if it just doesn't exist (or enough) and any dwarf with a preference for granite would be given a bedroom carved (and smoothed) into granite, if I desire to pamper them so. Where the bedroom's digging creates rock of a notably useful/interesting kind, I may shove a workshop temporarily into one of the rooms to make blocks or tables or mechanisms out of it, at least until I start to get residents filling up the place.
All bedrooms are individual, often four 5x5s per 'block of rock' layout, each has their own door and a nice rotational symmetry, per block, that gets reflected and translated around to other room-blocks in layout (entry plus all provided furniture). Where I provide a suite, that's four 5x5s with one edge-entrance into the office or dining room (chosen according to functional needs, from same furniture requirements), with dining room or office (whatever the first is not) in one direction and bedroom and tomb leading off of the other.
Furniture may start out as "whatever I've got made", but tends to become a consistant quality (for non-suites), or the very best available (for suites). Where/when possible, of the key material (the room's own rock, and/or a preference material; and I tend to choose a single wood-type at the start to reserve for all beds, special orders aside), and I'll mass-produce even doors, as soon as I have enough manpower free from basic survival issues, to give me that choice, and one or two future-bedrooms may be designated to the tables, thrones, statues, etc, that I'll eventually be placing or replacing (surplus quantities, probably those off-quality due to being less or more than that which seems usable) wend their way to the trade depot, if not another layer of bedrooms-in-potentia.
Where cavern-water is available, I carefully tap into it on its level to ultimately fill a cistern (single of multiple Zs of depth, shaped to fit 'block plan' and 'cavern wall' edges, and the needs of the digging out itself). Ideally this cistern acts as a 'waterlock' buffer between the untamed cavern and the further well-bottom cistern (accepts multiple wellheads dropped down from various locations in the Zs above, e.g. the hospital, wherever that is) as well as maybe a more standard bucket-dipping pool and/or bathhouse-type usable water-source. Floodgated links between and out of drainable 'wet-spaces' are designed in a manner highly dependent upon local geology and what else I've laid out, but have a general practiced form or set of alternatives (drains to map-edge or drains into next cavern down, for example, with supporting infrastructure and safeguards picked from a mostly established 'tapas' menu).
Wherever the magma is most accessible, thereupon I set up to tap it, and duct it below (and weaving between) the magmaworkshops. Around and above those (in ways previously described) are the stockpiles for ores, flux, any necessary charcoal (and source-type of wood) or coal-type fuel and of course the bars (product and intermediate material) and final goods chucked out of the final workshops in any given chain. All material destined for this magmaindustry layer is brought down (often the very bottom of the map, or practically so) and only final product is hauled back up, as needed, having done the refining and processing in a close-knit production-line.
Additional dining(/drinking) areas are dotted around the stack/width of the fort. Military training/mustering (depending upon if I'm doing it in one or other ways) may be centralised or spread about. I've had times when my archery ranges (and catapult-training ones) were in one whole (non-bedroom) intercavern Z-gap, criss-crossing each other like a grand hidden underground base (well, technically it was!), or I've just set up something simple near the core of the upper layers and left it at that. And some resupply stockrooms near (within the fortress-internal side!) the pillboxes and sally-ports, don't go amiss, with primarily food, drink and ammo hauled to them in anticipation. A more central Q-Stores for armour and equipment works best for me, though. (Or go collect it from the manufacturer! It's rarely an emergency, in my forts.)
...I think that covers my current design philosophies and tendencies. I can tell you about now defunct (but, at the time, finely honed) ideas, like how I used to set up my windmills (before I stopped using windmills), or my labarythine trap corridors to augment my subterranean wagonable link(s) from the surface to my beating-heart-of-the-fortress Depot, but with little need these days (or 'better' setups, or necessarily changed when wagons no longer went through trap-corridirs) I'll spare you that... 
