It's fairly easy to choose between the different plantations when the settler phase comes around as you just have to evaluate which you have the production capacity for or which you would be able to buy the production capacity for, and take into account what other goods you can produce and what other players can. However, Quarries are a little different, and sometimes I find it difficult to choose if I should take one or not. Here's some rules I use:
If I don't have 2 quarries yet and there's at least 4 builder phases left.
If there's no plantations I want.
If there aren't many left and I want to deny another player the privilege of having one.
Only take a 3rd or 4th Quarry if it will make a big difference in being able to get a very valuable building, usually from the third or fourth tier.
What rules do you use when determining if you should take a Quarry? What are the most notable situations when you should NOT take a Quarry when you are able to?