Bigger is better. The larger the diameter, the more creative freedom you have with your workouts.
Since you have more mat space to work with, you can do sit-ups or other workouts laying on it. Since the mat is a lot softer than the floor it will be easier on your back. The 44" offers a good balance of jumping space and overall size of the frame and is our most popular size. The 39" is great for its portability, but may not be large enough for a wide variety of exercises.