The obvious differences in 28 and 31 spline axles will be the number of splines! When you count the number of teeth (splines) on each axle, you can find out which option you have. 31 Spline Axles also tend to be larger in diameter to accommodate the increased amount of splines.
Most factory Solid Axle (Live Axle) Mustangs from 1979-2004 are equipped with the standard 28 spline axles regardless if the car is equipped with 4 lug or 5 lug. The keys to building the 8.8 Ford are pretty simple. If you are planning to make at least 400 Horsepower through the 8.8 Rear, the first step is better axles. 31 spline axles which are about 30% stronger than the 28 spline axles making them a popular aftermarket upgrade for Fox, SN95, and New Edge Mustang owners. The 28 spline axles in the 1979-2004 Mustangs will hold up to around 400 rear wheel horsepower before the sound of inevitability, the snap you hear when the axles break under heavy launching. Keep in mind that when you upgrade to the 31 Spline Axles, you will also need a 31 Spline Differential to match up with the new spline requirement!
Most of the Solid Rear Axle (Live Axle) on 2005-2014 S197 Mustangs are equipped from the factory with 31 Spline Axles. The 2005-2010 V6 Mustang 7.5" rear end still utilizes the 28 spline rear axle, while the 2005-2010 V8 Mustangs with the 8.8" rear end have the 31 spline rear axle. Starting in 2011, both the V6 and 5.0L Mustangs were equipped with the 31 spline 8.8" rear from the factory. Stock axles are adequate for daily-driving and most bolt-on upgrades, but if you are considering to have more than 500 rear wheel horsepower, you will want to look into upgrading to stronger aftermarket axles.