I always wipe out every jungle tile in sight ASAP, and oftentimes I still find the coal where the jungle was. There are strong incentives for clearing activities, and very little penalty for doing severe clearing, other than using up worker turns. At some point you might get global warming, but I rarely see that, even in a late modern games where the nukes are flying left and right. The global warming was much more severe in Civ2, you'd get these huge strips of useless territory wreaking havoc with everything, or lots of jungle and desert appearing. Civ3 encourages you to clear forests and jungles, with only having minor consequences for global warming. The strategic resources are the only ones that might deplete, but that happens regardless of your activities. Even then, it's only coal, iron, saltpeter, uranium and oil that disappear often. Horses never deplete, rubber might possibly, and maybe aluminum, but I've never seen it.