It depends on your goals, but in most cases, you want to do your cardio after your workout. I don't want this to turn into a chemistry lesson, so I'll keep it simple.
Cardio helps increase your heart rate which, after your workout, will result in more oxygen and nutrient rich blood getting into your muscles faster. This can help fight the buildup of lactic acid in your muscles (which is what gives you that sore, burning feeling the next day), and, if you take a protein shake, or other postworkout supplement, it'll help your muscles start the rebuilding process almost immediately.
If you're trying to lose weight, you will definitely want to do your cardio after your workout, preferably first thing in the morning before you've had anything to eat or drink. The reason for this is that your workout will use up almost all of the adenosine triphosphate (ATP) in your body, as well as the phosphocreatine in your muscles. This means when you start your cardio, your body won't have any energy left for your workout, this will force your body to use stored body fat for energy.