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 main 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.
Your decking fasteners are primarily working to withstand withdrawal. Walking across the deck surface places unevenly distributed forces on the decking and joists, causing them to deflect differently. The connection of the decking to the joists is constantly working to resist this differential and to pull the fastener from the joist. Screws are designed to withstand much more withdrawal forces than nails and are a better choice for decking installation.
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 material. Composite materials offer a variety of hidden fasteners choices, be sure to follow the manufacturers installation instructions.