A joule is derived unit of energy, heat or work. For your charger, think of it as the output. More joules = more shock.
You have probably seen the terms Output Joules and Stored Joules. Don't get these confused, and be aware of which is advertised on the charger. They are not the same thing! A charger may advertise 30 Joules, but only refer to the stored joules (A fence charger will always store more joules than it outputs). Stored Joules represent the amount of power stored inside your charger. This is ran through an output transformer, which converts the power to a higher voltage. Some of the power is lost during this conversion. Output Joules refer to the actual output of the charger - the power available to shock the animal.
Electric Fence Charger