I tend to go for a theme, then set a group of parameters i want and go for those. I basically gen maps for the parameters i want with the settings i want.
Say i wanted a fort built INTO a lake, so i look for freshwater lakes. To get lots of those, i crank up mountains and elevation variance while turning down the erosion and add lots of river start points (800 actually). This results in plenty of rivers that pool at the valleys between the mountain ranges, giving me plenty of freshwater lakes to work with.
Normally such a setup would be heavy on aquifers, 2 sometimes even 3 levels. So i have eliminate those from the raws as they do not fit into my currenct concept.
Since I will be building on flat lands, i increase the cave layer sizes, to get plenty of space underground, this way i can end up with 80+ z deep maps even when the surface is completely flat. Then it is just a matter of finding the ideal site: got to have sand, sedimentary layer, some kind of flux, a savage biome, access to all 4 civilizations, a decent 4x4 or 5x5 embark size with 2-4 tiles of land and the rest water.
Initial worldgen is ran for 100 years
Then there is embark time.
On embark i check the underground with reveal and the ore/rock numbers with prospector. Criteria is to have 2000+ clownite, 10000+ iron ore and some sort of high value ore (silver, gold or both) 10000+ coal bearing rock. It is a plus to have something fancy underground, like a fortress or some cool underground feature, but not an absolute requirement.
When im satisfied, i quit, regen the world with a decent hisotry and check again to make sure the extra time didnt cause any problems, like extinction of a race or such. When im not satisfied, i try to find another site to run through the same process, or gen a new world.
Thats my "process" of doing it. Finding a promising site usually takes between 2 and 4 hours of genning / checking for sites.