Gems add 2
to an unimproved tile. It's 1
more than silver and gold because gems cannot be improved by mint. And if gems are on a hill tile, you get +1
. Et voila, the best tile ever.
Generally, there are 3 types of resources: bonus, luxury and strategic. You'll lose bonus resources (except stone) if you settle your city on top of them. Luxury and strategic resources remain intact so it's not a last resort option to settle their tiles.
It's generally advisable to build on top of resources that provide for poor tile yield, like furs or ivory. Incense, wine, spices etc. also can fall under this category. As long as you would be unlikely to work the resource tile, it's better to settle on a resource because it will give you a small gold bonus. The perfect example of that is an incense source in a desert tile. You of course need to take into account such things like fertilizer in later game or goddess of the hunt.
Plots with strategic resources are usually better left outside a city to be worked by citizens later. They simply provide good yields that are also further improvable by various things. The best thing to do with them is to plant a great person on top of them. Great people's improvements connect strategic resources and add sizable bonuses to plt yield.