Potential Effects
Temperature: Cooler climates may encourage denser populations, closer home groupings. Warmer weather to encourage larger structures, open-air porches and awnings?
Materials: Not currently tracked, but sparseness of forestation or number of soil layers between surface and stone could drive up "invisible" cost of building (i.e. make private residences smaller, encourage multi-family dwellings, widen spacing of individual farms). Aquifers could make "quarrying" nearly impossible for world-gen sites.
Topography: Flatlands encourage sprawl, hills and mountains cause communities to try to conserve what flat land there is (especially since DF farms don't adapt well to rolling hills). Also implied economies (farming, herding, mining) attached to topography in such a way that they could impact spread and population density.
Water: Even without boats implemented, fishing villages could still prefer to cluster around a spot on the shore or riverbank. Boggy or swampy soil might make for small hamlets of subsistence farmers and a smattering of hunters/fishermen/lumberjacks living in the midst of things or in distant shacks on the edge of town. Very dry ground conversely favors nomads or loosely clustered ranchers. Rivers could be linked to purely theoretical trading going on in the civ.
Wildlife: There is safety to be had in numbers.
cont
Capital Vs. Border: Ditto wildlife. Also, having a larger portion of the population involved in military and government necessitates a support network close at hand to keep them supplied with goods and services. Could translate to a tendency for capitals and border forts to maintain city walls and a large number of farming communities spread out around them.
Wealth: Difficult to keep track of in fortress mode, let alone a worldgen town, but it seems likely that shop owners would have fancier (or at least bigger) houses. Temple housing could also be pretty ritzy, or even translate into little monasteries (which would be cool to scatter around the wilderness a bit as well). Medical specialists, nobles, mayors and commanders might as well have some kind of "wealthy" neighborhoods or manors away from the tenements full of peasants, soapers, fish dissectors, etc.
Culture: Goblins probably snatch so many babies because they can't stand letting that drafty old tower stay empty all day. Elves, on the other hand, loathe breathing the same air as someone else so much that they don't even build houses for fear of accidentally trapping someone's stale dwarf breath where it might be smelled. Entity Preferences in general seem like a good candidate for influencing population distribution and density.
Roads: The wide-open and empty arteries of "commerce" supplying the lifeblood of every theoretical economy. Populated intersections or riversides might attract skilled craftsmen to drive up the invisible wealth of a region. Well-populated and interconnected border forts could become very valuable in worldgen, leading to large investments of military and political power from both neighboring civs (translation: forts, walls, barracks, offices, bridges, markets, inns, etc.).
Insane Mayors: Mandates already drive the game in unusual and hilarious directions, so having a human mayor decide that no house may be above a certain height or located a certain distance away would make for variety in architecture and layout that might not occur on its own. Individual preferences would be most relevant, I guess, with a preference for circles leading to round houses or a preference for dwarfs causing a sudden upswing in underground dwellings and fire.