What are subs for?

Educate me: what is the purpose of submarines in the game? (Excluding nuke subs.)

Sure, T1 subs have some uses: raiding underwater mexes, maybe doing some damage to frigates (mostly before the opponent has T2 air/navy).

Destroyers are a strong counter to basically every sub (well, maybe not Atlantis), and torpedo launchers are a hard counter (except where the sub has a higher tech level and therefore more range).

Punishing someone who builds only cruisers? Sure, though frigates are also an effective counter.

Stealth? Yes, but (a) scout/spy planes can spot them and (b) a stealthed sub army isn't actually very useful. (Maybe it would be more useful if they could hit all T1 engies without having to surface, but not a major thing.)

I'm 1100-1400 ranked and don't play a lot of navy, but when I do, subs (especially T2 and Seraphim T3) don't seem to have a lot of use.

T2 subs fully counter phim navy up to t3 and all of UEF navy if it does not have lots of coopers.

Looking at the stats:

• All destroyers have ~100 DPS torps except UEF which is 30
• Cybran and Aeon have 2 anti-torp shots per 3.8s, Sera has 1 per 3.8s, UEF 2 per 10s
• Sera and Aeon destros have ~210 DPS on main guns, Cybran is 230, UEF is 275; Sera and UEF have range 60 vs 80 on the others
• The Cooper has approx the same torps and anti-torps as Cybran and Aeon destroyers, at ~25% the HP and 40% the mass cost
• T2 subs have 90 (Aeon) / 112 (Cybran) DPS but significantly worse anti-torps (2 per 7.7s for Aeon, 2 per 20s for Cybran); Cybran has stealth but also less HP; both cost approx half a destroyer but with much less HP (~25% for aeon, 20% for Cybran)
• The neptune (T3 destro) has 2 anti-torps / 10s and only 20 DPS torpedo
• The T3 sub has 335 DPS torps and 2 anti-torps / 6.7s at 50-60% the HP of a destroyer and 133% the cost (or 220% the HP, 270% the cost of the Aeon T2 sub), which should make it cost effective vs any destroyer, provided the destroyer isn't able to use its main guns and there are no torp bombers

Conclusions:

• The stats back up FtX's point
• The Seraphim destroyer is in many ways the worst (though beam weapons have some advantages, provided you aren't trying to kill land targets over a small cliff)
• Subs are still only good in the absence of torp bombers due to low HP

Mass t1 subs are anti meta, it's not a good option on paper but since your opponent isn't expecting it it can win you navy against cybran and uef via bypassing the frig spam and killing production (only if torp bombers are not in play)

a pack of T2 subs are ok for hunting key targets in the opponent navy like shield/stealth boats and cruisers

in my experience (1400-1600ish ladder) subs can be sometimes useful early on if you know what you are doing and don't overbuild. Not the main thing and not something you'd build every game, but especially since the opponent doesn't expect it you can get some free damage on frigs that are far from navy hq and if he can't react quickly enough for some other reason(air advantage, can't afford t2, not enough apm while u drop at his base or smth)

edit: also, it's a rare thing but as far as I remember some subs have laser whose range is greater than frigs and on certain maps that's the only way to raid certain mexes with navy early on

In addition to what others have written:

Subs can kill T1 mexes on maps that have water mexes. this is a big deal on those maps. Taking/raiding T1 mexes is a major part of competitive gameplay. It's not less true when the mexes are underwater.

Subs can be used for killing ACUs. ACUs can get pretty cheeky when they think it's safe to duck into the water.

More advanced as an addition:
If you're Aeon, you can build subs instead of frigs. Cuz:

• Aeon Frigs suck
• Your opponent builds counter-subs at one point -> You just stop building subs -> Their subs are basically useless against your frigs and your destro just rapes them
  However make sure to vary that strategy and not always go for subs as Aeon.