Cities tend to grow organically. The oldest part of town will have once been a barbarian encampment. The oldest streets used to be trails, maybe even cattle trails.
The newest and best planned part of the city will be the part that was afflicted by flood or fire most recently. Plague possibly, but only if the new residents sterilized the old ground by burning down the buildings. If your city has a "dwarf quarter," they probably rebuilt the buildings to suit themselves. Lots of cities have walls, but if those walls have been in place more than 50 years, the city has at least partially outgrown them. It may have outgrown them by the time the walls were complete. And the dwarves have probably tunneled under them in any case.
Much can be decided by the needs and priorities of the city's rulers. Are roving traders assumed to be a source of thievery? If so, then there is likely to be a caravan camp outside the city walls, and traders aren't allowed inside the walls after nightfall. If that system has been in place a long time, you may have a permanent bazaar/souk outside the walls that is larger than some of the city's districts. If religious infighting has been historically a source of violent conflict, all temples may be required to be outside the walls. If one is by far dominant, especially if it is the chosen religion of the city ruler, it may be the only one whose clergy is allowed within the walls, and there may be a chapel attached to the local citadel.
Basically it amounts to asking yourself how did it start, how did it grow and why, and what do the people who live there want? Don't leave magic out of the mix. If there is cheap and simple magic available in your game that would make the city cleaner, more prosperous, more efficient, etc. then it makes no sense not to have it in use. An obvious example is street lights.
Lastly, yes jdale is right, NBOS software makes some good stuff, they are well worth looking into.
NOTE: Dallas, TX began life as a Native American encampment. Why? Because a ridge of rock passed under the Trinity River at that point, making it one of the few decent river fords for many miles in either direction. Upper and Lower Vicksburg were for most purposes 2 separate cities, one at the top of the bluff and one at the bottom. Start with geography and figure out why people want to live there in the first place.
