Skilled freerunners don't just stop and ‘catch their breath' during a run, and neither should you, so you'll want to work in some endurance training to your routines. Longer runs (or workouts) will get your body ready to go the distance, as will pushing your limits by doing some of your training while you're completely gassed and ready to drop. There are a lot of different methods to endurance training, but one way to be sure yours applies to your parkour is to focus on training the moves and sequences you actually use (and not just spend hours on a training bike in your basement).
Many of the powerful moves of skilled traceurs demand extra strength that you're not likely to develop during most bodyweight workouts, so hitting the barbells for some added resistance can really increase your strength. Most strength training programs focus on big muscle groups and full-body movements, such as the squat, the clean-and-press, the military press, and the deadlift, although there are at least as many different types of strength training exercises and routines as there are personal trainers, so you may have to experiment to find what works best for you.