Dwarf Fortress World Generation
Dwarf Fortress achieved much better results by handling fields separately: temperature, rainfall, elevation, drainage, etc. The interplay of those fields determined the final biome, resulting in a more natural, internally consistent solution. — Tarn Adams
Dwarf Fortress generates worlds with complex biomes similar to Minecraft. As apposed to attempting to generate the biomes directly from a seed and Perlin Noise, he opted to generate the constituent parts of a complete world simulation. Features like rainfall are much easier to simulate through a combination of random generation and rules. The random generation might dictate where precipitation exists initially, whereas rules like mountains blocking high moisture winds, reducing rain in the shadow of a mountain, can be added to the system to improve realism.
The noise may also be interpreted differently under certain conditions. Precipitation in freezing temperatures could result in a snowy climate, whereas lack of precipitation in the same environment would result in a tundra. This is an example of allowing the two systems to operate separately, but using their combined outputs to derive their results. Another possibility is that one system effects another. We've already seen elevation affect precipitation, in the form of mountains and rain shadows. Another example is drainage, which would almost entirely be based on a combination of elevation, precipitation, and some randomization. This drainage might then be used to alter elevation in the form of erosion, creating a cycle of interdependence.
In some cases, the state of the systems might be allowed to stay separate, and the combined effects would only be interpreted later. In the case of the mountains rain shadow. You might allow the precipitation system to keep its state, but combine the amount of rain the precipitation calls for with the intensity of the mountains shadow, in order to determine the true rainfall of the region.