Using Stoneskin can differ depending on the situation. If you get WHM or SCH to 50, you will probably find you use it a little more.
My general rule of thumb is:
At the start of a dungeon/instance I will put it on everyone. If it is a multiple monster dungeon/instance, I will reapply it to everyone before each 'boss' battle. This means I can usually get all of my DoTs on the monster as I probably wont need to cast a Cure.
In certain fights you can add it to tanks before a large attack is coming. Examples could be: Everyone's Grudge on the Tonberry King Last Boss in Wanderer's Palace or Final Sting from the Temple Bees in Sunken Temple.
Also if you are doing fights with 2 healers, the tank may not need a heal from you at a point, so popping on a Stoneskin instead is good practice.
Continued below due to character amount restriction:
