I noticed that Aeon submarines can surface (not sure if other factions' subs can do that, too). My question is, why would I want to surface? I can't see any reason why this possibility was introduced, as then more units can attack them.
There are occasions when it is very useful to surface a fleet of subs to take out some shore-based object or engineer. And iirc all factions can (no idea about the Zephyr - I stopped before then).
I (when I used to play SupCom years ago) would often use them to destroy shore-based AA to allow my bombers to come over. On archipelago maps and maps with strategic islands seperate from the mainland (my favourite map - Seton's Clutch - had these) I find this feature very useful. They will not cope against concentrated land defences and ground troops such as would be found on the mainland.
Against a few ships with anti-torps then a submarine may actually be better off surfacing. They do have a plasma cannon on after all, which does reasonable damage and at reasonable range.
You can infiltrate a small fleet of 10+ subs and have a flexible force that can sink docks, take out shore defences, and most importantly choose when to engage.
They are not designed for prolonged heavy firefights, so use surfacing tactically and probably infrequently.
edit: I am talking about the basic subs. The poster above is correct that some have special features that require surfacing.
Some submarines can only use their abilities on the surface, such as the T3 Strategic Missile subs and the UEF Atlantis Experimental Aircraft Carrier.
You can also sometimes use a submarine as a decoy, surfacing to draw fire and then diving to escape.
Some submarines also have anti-air/anti-surface weapons that can only fire when surfaced.