UEF Tigershark: The Tiger Shark is the toughest of the four subs. Having a whole 600 HP. With a torpedo DPS of 38 and a cannon DPS of 25 the Tiger shark is decent. It fires salvos of two torpedoes doing 75 damage each. Its plasma cannon is useful on weakened units and hover units.
Cybran Sliver: Firing salvos of three torpedoes, and mounting a light laser, the Cybran submarine is a middle of the road unit. It has a marked advantage against the Seraphim sub as it fires more torpedoes than it's counterparts. It also has more HP than the Seraphim. It does less damage though when surfaced than the UEF submarine.
Aeon Sylph: The Sylph holds true to Aeon design and is useless against anything other than ships. It only features the second highest health and Torpedoes, which are equal to the other factions in DPS. Thus it gains no advantage other than comfort that it will never surface. It is basically a weaker but just as expensive version of the UEF tigershark, as it lacks a surface gun and has less hp. However, it does have more hp than it's cybran and seraphim variations.
Seraphim Sou-istle: Being the lightest sub, the Sou-istle is somewhat lacking in HP. It does however have the most goodies. It features a Torpedo launcher identical to that of the UEF and Aeon. It also has a deck gun that is the middle ground between the UEF and Cybran submarines. It's biggest perk is an anti-torpedo charge. It does not fire fast enough though to give it a real advantage. It is still useful in naval engagements nonetheless.
Note that the mass costs are doubled in the Forged Alliance campaign (compared to those listed here), which makes them a pretty poor investment in that environment relative to just about any other naval unit.