I stick to an 'invisible grid' pattern. Basically, after much trial and error, I arrived at an imaginary grid of 7x7 squares in a grid separated by 1 tile dividing walls. This is grouped in 3x3 sets of the 7x7 squares surrounded by a 7 wide corridor. So something like:
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Everything is designed on this block, with each block's corner towers and hallways overlapping. As long as my rooms fit into a multiple of a 7x7 square, everything will always fit together nicely. The standardized hallways and towers of stairs at the corners ensure dwarves have access everywhere. The modularity means I can designate a large section of the fortress's overall design, but keep sections cut off until they are needed with little more that a 1x3 strip. It is also just about the right size for your first year's fortress, provided you dig larger hallways and use them for storage before you get to fancy them up. I've trial-and-errored my way to a 'toolkit' of room floor plans that are easy to remember how to build because of the regular geometry. There are 7x23 halls, 2x2 quarters complex (48 dwarves in one block ), a one block palace, 7x7 stair tower, one-block warehouse, one block rotunda, 2 block grand hall, and the catacombs. Military installations are simply less-ornate versions of these.
Also, since every stair tower is a known distance from the next, as long as you know where the stairs are, you can layout constructions above ground that line up easily with the tunnels below.
Plus it looks pretty great with an angled wall tileset.