I was thinking about this recently too. Id like to see some disasters based on location and climate introduced into the game. I use a Mac, so havent even yet gotten to enjoy the volcanos in the Windows-only C3C.
Volcanos could appear in certain mountain ranges, some recognizable from the get-go, but some might appear by surprise from a normal-looking mountain. If you were foolish enough to build a city right next to a volcano, youd have a fair chance of it being destroyed by eruption after a few thousand years have passed. If you built it a couple tiles away, youd be likely to get eruptions occasionally destroying farmland and improvements nearby the mountain, but your city might only suffer economic and health problems in those cases rather than destruction. Building a city right next to a volcano would basically be a long-running game of Russian Roulette. You would eventually find the bullet. It shouldnt be done.
Earthquakes would be great to add, and would tend most often to happen along coastal rim areas, but could be possible anywhere ultimately. Cities on coasts have great advantages of trade and sea-based food supplies, etc. but face increased likelihood of larger earthquakes which could either damage structures and cause monetary penalty or even knock down, say, your cathedral and cause it to have to be rebuilt, as well as your city getting knocked down a few population points. A tsunami would also possibly (but not necessarily) follow an earthquake on nearby costal areas and wouuld ruin farmland and improvements and maybe also knock down some city strutures and cause your harbor to have to be rebuilt, etc. Tsunamis would also affect cities further away, including ones in other countries, even if they were not affected by the earthquake itself.
In the grasslands, plains and deserts, tornados could appear and destroy terrain improvements along a path of travel. If a tornado crossed a city, similar results to those of an earthquake would result. Typhoons and hurricanes could also occur in appropriate coastal latitudes. Climate shifts over centuries or millennia could change some terrain...an entire region or latitude of grassland could become plains or vice-versa at some point, but also might shift back later. Forests would grow or go away. Ice or tundra might move down or up in latitude for a while. Im thinking about the mini ice age in Europe in the middle ages, the year without a summer, etc.
I think this would be great fun and introduce these kinds of gradual or occasional variables into the Civ world, instead of knowing exactly what you can expect out of city once built for the next 6000 years because you can see the terrain around it.