SAMS are good defenses for your main base as well as other things you would expect T3 bombers to attack, as no non-experimental unit can survive being hit by multiple SAM rockets (gunships are an exception). There are inconvenient things though such as the fact that SAMS have a slower reload time and target a single unit, thus SAMS are prone to overkilling a target and aren't as good at taking out swarms of low-tech units as flak is.
SAM positions are easiest to destroy from the ground since they don't fire at ground units, however they are almost always defended. If you encounter a SAM that you can capture easily though it is almost always good to capture since where it's placed to be an inconvenience for you it will now hurt your foe. The other way to destroy a SAM is by swarming by presenting too many targets for its single target rockets to shoot at, or, and this is extremely costly you can send a first wave of cheap units to distract it and then hoping the second wave comes fast enough then destroy it with better units in wave 2.
The Seraphim T3 Anti-Air Defense is widely accepted to be the worst of the four. While it has the same DPS, its projectiles do not track, leading to a far, far lower Effective DPS. However, while it may be inferior against fast fliers such as Spy planes or ASFs, it's high muzzle velocity increases the chance of killing Strategic Bombers before they have a chance to drop their bombs.
The Aeon T3 Anti-Air SAM Launcher has a low rate of fire, but high accuracy - making it the most effective at taking down both experimentals, and "large" aircraft such as gunships, but meaning that it often needs support when pitted against weaker aircraft in larger numbers. It's stats are the same as it's seraphim counterpart, but it has tracking projectiles and does not immediately show up on radar like seraphim structures, making it superior in every way.
The Cybran T3 Anti-Air SAM Launcher has a higher rate of fire - firing more projectiles per salvo, allowing it to take down more planes, making it arguably the most efficient of the T3 SAMs. Its missiles are fast and accurate, although not quite as fast as the Aeon's version, the number of them more than make up for it.
The UEF T3 Anti-Air SAM Launcher fires the most projectiles - making it best able to deal with large numbers of enemy aircraft - meaning that it'll scale well against lower techs far better than the others. Its missiles are not as fast, nor as accurate as either the Aeon, nor the Cybran versions, it is still a very respectable structure in its own right, but should not operate without backup flak guns.