SimEarth 2000.
Needs a good, modern computer to play, but graphics are maybe at the level of Civilization III. Maybe. Why? Because it uses all that computing horsepower for just with sheer number crunching. You’d have the ability to modify anything about a planet, just to see what would happen. Like if, say, you wanted to have a planet half the size of Earth but with three times the mass, 3 AUs from an F-type star, and with a biosphere supporting a species of chlorine-breathers who have an industrial infrastructure generating alarming amounts of Helium pollution. And with a generous plugin and editor system allowing the users to hack the simulation engine to any number of extremes.
And another project, currently unnamed…think of the battle between the rats and soldiers in the Nutcracker crossed with Army Men 3D. (Or The Mouse and his Child crossed with 1632. Only with more broadswords and air support.)