If you are using wood decking you will have to make the decision on what type of fasteners to use.  Using nails will greatly speed up the process by allowing you to use a pneumatic nail gun.  The only drawback is that deck boards that are nailed can begin to squeak as the wood dries out and shrinks.  Using screws for installing your decking will require considerably more labor but can result in a cleaner surface.  Deck screws come in a variety of colors and styles.  Trim head screws work well to disguise themselves in the flooring.  Wood that is screwed into place may develop small cracks where the screw split the wood. 

Always make sure your fasteners are approved for use with new pressure treated lumber and are the appropriate sizes for your application.  Some hardwood decking will require you to predrill before installing fasteners to prevent breaking screws in the dense surface.  Composite materials offer a variety of fastener choices, be sure to follow the manufacturers installation instructions.