General layout lessons I've learned after a couple months of play:
-If you want something that just works, make your production area large and open, like an enormous factory floor. Walls get in the way more often than they help. This does not apply to refuse piles.
-Put all of "hands-on" stuff (production, depot, barracks, stockpiles, control room, anything you need to work with frequently) on the 1st-3rd levels. This minimizes the time I spend clicking between Z-levels.
(A cube would be more efficient dwarf-wise, but I find 3 or fewer production floors to be easier on me as a player.)
Hands-off stuff like bedrooms, tombs, and other build-and-forget stuff can go on lower levels. Bedrooms get the bottommost level (or Z-16, whichever comes first) to make absolutely sure they are insulated from noise.
-I'm not quite sure how to word this but... If you are building a cube/factory-floor fortress, and you want to have stockpiles of items that you don't want dwarves using in a workshop (for instance, if you want to keep bauxite away from your craftsdwarves), then be sure to dig out a cavern a large
horizontal distance away that you can put them in.
Because of the way dwarves choose the "nearest" item, a craftsdwarf will take a piece of bauxite in a stockpile 16 Z-levels down at the very bottom of your fortress over a piece of granite sitting 17 tiles away (and he will gladly walk thousands of tiles to get that bauxite if he has to). It is much easier to put items "out of range" on the xy plane than it is to put them out of range on the z plane, because you generally have far more tiles to work with on the xy plane.
So moral of that rambling advice: Make a cavern a large
horizontal distance away from your workshops, and use it to store stuff that you're reserving for special projects/moods/etc. The cube generally will not suffice for this.
-Smaller barracks equal faster training. Smaller dining rooms equal more socializing. Adjust your plans accordingly.
-Speaking of barracks, sparring dwarves will drop clothes on the floor, and never pick them up, and they cannot be dumped. Thus any space you make into a barrack has a good chance of becoming useless for any other purpose unless you make provisions for flooding it with magma, or build some atom smashers on the floor directly below to drop clothes into via channeling. Design accordingly
-Speaking again of barracks, design your layout so that people entering/exiting the fortress have to pass through your barracks to do it.
-Finally, if you want to take the utilitarian cube fortress and make it better looking, grab the script by Rysith on
this page, and turn your cube into a cylinder, or spire, or something. It keeps most of the advantages of the efficient-cube formula, but for me at least, it makes the fortress feel a lot nicer, more professional. I don't know why, but it does.