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[Lucky33]

Accelerated Shields:  Core hullmod for anything big what supposed to get into brawl.
Additional Berthing:  Never used this one. Even while raiding the whole sector out of civilization.
Advanced Optics:  So-so.
Advanced Turret Gyros:  Like to have it if I have some spare OP.
Augmented Drive Field:  Exploration drive. Usage on combat ships is limited to some very specific cases.
Automated Repair Unit:  Core hullmod for the most of my ships.
Auxiliary Fuel Tanks:  So-so.
Auxiliary Thrusters:  Core hullmod for the brawler Onslaught. Its even in the sim variant.
Blast Doors:  Used only in testing. Good for that purpose but never put it onto the real variant.
Converted Hangar:  So-so. Its mostly like walking in circles around this mod.
Dedicated Targeting Core:  Core hullmod till ITU.
ECCM Package:  Core hullmod for missile builds.
ECM Package:  Core hullmod for the ranged builds. Considered important even for brawler builds.
Efficiency Overhaul:  So-so. Its kinda inverted in its stats. Minor boost to logistics, huge boost to post-battle recovery. Prefer to have it other way around.
Expanded Cargo Holds:  Core hullmod for early game. Like very early. After that I never use it again.
Expanded Deck Crew:  Its more like "fighter spam factory".
Expanded Magazines:  Core hullmod for any weapons boosted by it.
Expanded Missile Racks:  Core hullmod.
Extended Shields:  So-so.
Flux Coil Adjunct:  Sometimes its usefull.
Flux Distributor:  Sometimes its usefull.
Hardened Shields:  Core hullmod.
Hardened Subsystems:  Its more like tax for the small ships.
Heavy Armor:  Surprisingly useless mod. Cost is too high, drawback is too high. I mean it will be good if every mod was balanced that way but they dont so why even bother?
High Resolutions Sensors:  Good for the roleplay.
Insulated Engine Assembly:  Good for the roleplay.
Integrated Point Defense AI:  Core hullmod.
Integrated Targeting Unit:  Core hullmod.
Makeshift Shield Generator:  Never used it.
Militarized Subsystems:  Core hullmod.
Nav Relay:  Core hullmod for the "admiral" skill set.
Operations Center:  Core hullmod for the "admiral" skill set.
Recovery Shuttles:  Never used it.
Reinforced Bulkheads:  Thats what is expected of the "heavy armor" hullmod. Core thing for AI tanks. Not really a core for a personal ship but still used.
Resistant Flux Conduits:  Core hullmod.
Safety Override:  Core hullmod. Game is like: do you want to fly around and kill stuff? And Im like: Yes.
Shield Conversion Front:  Sometimes its usefull on some ships.
Shield Conversion Omni:  Core hullmod on the brawlers.
Solar Shielding:  Core hullmod.
Stabilized Shields:  Core hullmod for the high tech.
Surveying Equipment:  It does exactly that it says.
Unstable Injector:  Core hullmod for some specialized builds. But for them its the difference between "it works" and "it fails miserably".

[SCC]

I wouldn't mind having ECM and nav relay available from the start. They already are hardly desirable and mostly obsoleted with skills, so maybe they could get some use in the early game.
Blast Doors and Recovery Shuttles can go. Alex likes to think the players aren't ***, but they are, and crew turnover is only an issue, of you're too far away from a space port.

[Lucky33]

Mainstay of the real fighter spam are drone fighters. No crew losses. Ship's crew losses are negated by the skills. Trading something really important for the Blast Doors may result in even more losses.

[TaLaR]

Accelerated Shields:  Excellent for player-piloted larger ships, more so with omni shields. Worthy for AI omni shielded capitals too.
Additional Berthing:  Obvious pick for crew transports.
Advanced Optics:  TL Sunder or Paragon.
Advanced Turret Gyros:  As long as ship has enough turreted weapons with medium to low rotation speed, this is likely to be useful.
Augmented Drive Field:  When you have few ships larger than the rest of fleet.
Automated Repair Unit:  I see how it can be useful to reckless SO brawlers, but don't use builds like that.
Auxiliary Fuel Tanks:  Obvious pick for tankers.
Auxiliary Thrusters:  Can be useful, but somewhat overpriced for what it does.
Blast Doors:  Had to check exact effect on wiki. So yeah, I don't use it, crew is cheap enough.
Converted Hangar:  It's powerful for Buffalo mk2 or Valkyrie spam, but you can't do that in campaign. Good for Enforcers too. Too OP-inefficient for cruisers or capitals.
Dedicated Targeting Core:  If I don't have ITU.
ECCM Package:  For missile builds.
ECM Package:  I see how it could be useful, but EW1 is usually enough without it.
Efficiency Overhaul:  So cheap that I'm sometimes tempted to use it even on direct combat ships, especially considering faster CR recovery.
Expanded Cargo Holds:  Obvious pick for cargo ships.
Expanded Deck Crew:  Carrier ITU, as others said.
Expanded Magazines: If you have 2 or more Autopulses.
Expanded Missile Racks:  For missile builds.
Extended Shields:  Mine protection for ships that don't have slots for proper PD. Otherwise they tend to take lots of unnecessary losses against stations.
Flux Coil Adjunct:  For phase ships.
Flux Distributor:  Any ship that can fit it without compromising build.
Hardened Shields:  I might use this even more than ITU (because frigate ITU is crap).
Hardened Subsystems: "Its more like tax for the small ships."
Heavy Armor: It is somewhat useful on an Onslaught and less so on similar low-tech ships. Problem is, AI doesn't use armor aggressively to win flux wars anyway.
High Resolutions Sensors:  Only if I get it for free with the hull.
Insulated Engine Assembly:  Occasionally used to compensate D-mods.
Integrated Point Defense AI:  IR Pulse + IPDAI combo.
Integrated Targeting Unit:  Every CR/Capital, most DEs, crap on frigates.
Makeshift Shield Generator:  Net negative. Ship with this wastes flux that could to weapons on crappy shield and has less speed (a lot more than you'd think, due to less efficient use of zero flux boost). Only useful to counter non-massed Tac lasers (massed would crush inefficient shield anyway).
Militarized Subsystems:  Any civilian ship that would drop fleet speed or raise sensor signature otherwise.
Nav Relay:  On combat-size 500, reaching 20% is not a problem without it. I guess it could be useful for small battle size.
Operations Center:  Don't like the playstyle.
Recovery Shuttles:  Crew is cheap.
Reinforced Bulkheads:  When I have nothing better to put on an officer-less ship.
Resistant Flux Conduits: Core for player ships. Much less useful for AI.
Safety Override:  Strong, but I rarely use it in campaign.
Shield Conversion Front:  Stabilized, Accelerated and Expanded all in 1. Still, losing omni and OP-cost make fairly niche.
Shield Conversion Omni:  Too expensive considering the downsides and that front-shielded ships tend to be built around hardpoints anyway.
Solar Shielding:  As far as I remember it doesn't affect shield damage in current release. Will become a must in next one with shield damage reduction.
Stabilized Shields:  Some ships like Paragon have too high maintenance otherwise. Also can be used in combination with other hullmods to max out soft flux resistance.
Surveying Equipment:  "It does exactly that it says."
Unstable Injector: Auto-pick for most frigates. Also DEs If don't have access to ITU yet. Very niche on larger ships.

[Megas]

Forgot one hullmod:  Armored Turret Mounts!  I do not use that due to more important picks.  The few times I considered getting it, would have slowed turn speed of slowish weapons (like autocannons) enough that I would need Advanced Turret Gyros too, and that would have made the whole package too expensive for the benefits.

I wouldn't mind having ECM and nav relay available from the start. They already are hardly desirable and mostly obsoleted with skills, so maybe they could get some use in the early game.

They might not be obsoleted by skills next release if skills no longer give bonuses just from deploying ships.

[Lucky33]

The fact that you forgot it and nobody really cared to fix it is a comprehensive characteristic by itself.

[Megas]

The only reason I would get Armored Turret Mounts is the minor armor bonus.  If I am concerned about weapons and engines getting knocked out, better to get Damage Control 2 skill and Automated Repair Unit to be almost effectively immune to knockout because they recover so fast.

[Lucky33]

Exactly. ARU costs as much as AWM but provides much more utility.

[Plantissue]

Armored Weapon Mounts are useful where there are no shields. I use them on phase ships and on the Conquest. The Conquest is an interesting case as it has narrow shields so the shield mods can be useful for them.

Automated Repair Unit is a bit of a strange one. I've tried using it on Conquest in case of EMP weapons and in theory it is useful when you want the protective qualities or stack on top of Armored Weapon Mounts and Insulated Engine Assembly, but in practice I find that preventing the disabling is more useful. To this day I am uncertain whether the increased durability of Armored Weapon Mounts and Insulated Engine Assembly helps against EMP weapons, but they certainly seem to help against weapon damage.

[Thaago]

Insulated Engine Assembly does help against EMP damage to engines - I'll use it on early game player SO ships just to stop flameouts (which are sometimes boring, sometimes instant death).

[Megas]

I would not use Automated Repair Unit on ships without Damage Control 2.  Half only is still a bit too long, not worth it instead of a more useful hullmod or better flux stats (to help kill things before my ship takes a hit).  When it is quarter with both hullmod and skill, then it is really nice because enemy does not have enough time to do anything significant before weapons or engine get repaired.

[RustyCabbage]

Accelerated Shields: I dunno, I've yet to see a situation where I felt it was worth the OP cost, but I admittedly don't pay a huge amount of attention to this.
Blast Doors: Crew is dirty cheap; I basically always prefer Reinforced Bulkheads. Maybe if it were cheaper, like 4/8/12/20 or even less.
ECM Package/Nav Relay: The former is rarely necessary with EW1, and the latter is unnecessary with whatever the skill is called. Maybe the skill rework will make this more enticing?
Expanded Deck Crew: Honestly just breaks carriers in terms of balance. Autogenerated fleets can't really abuse its compounding effects either. I think removing it would be a good step to dealing with fighter balance.
Extended Shields: I use it rarely, but it feels expensive for what it gives. Would be nice at 3/6/9/15.
Hardened Shields: Either too strong, or Heavy Armor is too weak.
Heavy Armor: Would probably be fine without the maneuverability penalty, but for AI control will basically always be inferior to Hardened Shields. Also it's weirdly undercosted for cruisers?
Operations Center: Too expensive for what it gives. I think it might be cool if it had scaling OP cost and effect like the other hull mods, though that might disrupt the style of gameplay it's used for too much.
Recovery Shuttles: Crew is still dirt cheap.
Shield Conversion - Omni: Why does it cost more than Shield Conversion - Front? As is, I don't see any cases where it's worth the cost.

Everything else seems more or less fine imo, or at least not notable enough to be worth commenting on.

[Serenitis]

Re: Blast Doors and Recovery Shuttles
Whilst crew is incredibly cheap and effort free to obtain, it does have a requirement that is not always possible to meet: You must be within range of somewehre that has crew available.
This is not always a guarantee given a possible focus for the player is exploring derelict and deserted regions far from any habitation.

Blast Doors is a 'nice to have' mod, which is often eclipsed by Reinforced Bulkheads due to the utility of being able to recover lost ships.
I'd like to use it more often, but rarely have the OP to do so.
When I do use it, it will likely be on my flagship if I'm expecting to take an aggro role. But it will be removed once the Damage Control skill is unlocked, which does the same thing for zero OP cost.
I would have no problem with Blast Doors and Bulkheads being merged.

Recovery Shuttles is something I use quite a lot. Carriers are usually a large part of my fleet, and fighters are a huge crew sink.
It is very easy to run a fighter heavy fleet's CR cap into the ground via combat losses, meaning you have less combat options and thus less salvage options.
This will always result in the exploration being abandoned in order to replenish crew, which can involve a non-trivial amount of travelling.
It is possible to recover crew from derelicts and debris fields, but any attempt to rely on that would be rather foolish.

Using drone fighters is an excellent way of sidestepping this issue. But that requires some initial action in this direction.

Re: Automated Repair Unit
I've never really cared about using this, even if I am routinely getting my ships shot at.
Why?
Because the Damage Control skill does the same thing for zero OP cost, and I already can't afford to fit the things I want.
And the same DC skill gives you free repairs at the end of the battle, which the ARU doesn't.
ARU basically doesn't have a hope of me ever using it because the Damage Control skill does more for less cost, and doesn't gimp my outfitting choices.

And, I'm still not over the fact this thing doesn't repair the hull in battle. #NaCl

[Plantissue]

For Recovery Shuttles, the way I see it is that if you are away from a source of crew, you are out exploring and shouldn't being doing any real amount of fighting. In fact since you aren't fighting, it doesn't even matter that much if your ships are undercrewed slightly as it doesn't affect your ability to survey and salvage. In any case you lose supply automatically when fighting, so it's not any different to buy crew when fighting.

The hull increase in Blast doors is much smaller than that of Reinforced Bulkhead, so you will only really get Blast Doors after Reinforced Bulkhead. If you are concerned about crew loss from ship damage, it is better to spoend that OP on defences so the damage doesn't occur in the first place.

Insulated Engine Assembly does help against EMP damage to engines - I'll use it on early game player SO ships just to stop flameouts (which are sometimes boring, sometimes instant death).

/good to know thanks. I'll assume Armored Weapon Mounts does help against EMP as well and will continue to use it.

[Megas]

Re: Automated Repair Unit
I've never really cared about using this, even if I am routinely getting my ships shot at.
Why?
Because the Damage Control skill does the same thing for zero OP cost, and I already can't afford to fit the things I want.

They stack.  If I want to use Automated Repair Unit, I want both skill and hullmod for near-instant repairs.  If my ship does not have Damage Control 2, then sure, ARU is not worth it because half repair time is still too long to wait for the OP spent.

ARU never repaired hull, only pre-0.8a Damage Control 10 did that, and it was game-changing overpowered.  It was the first Combat 10 perk I took because it was the biggest enabler of soloing fleets.  No longer could your flagship be worn down by damage attrition.

P.S.  However, old Automated Repair Unit used to cost double (because it did faster in-combat and campaign repairs), before it was split into its combat self and campaign Efficiency Overhaul.  Also, during the pre-0.8a days of Logistics, Automated Repair Unit was terrible because it added the drawback of raising Logistics cost of the ship by (I think) fifty percent, which meant smaller fleet before player hits Logistics cap.  It was better to bring two ships, like Onslaught and Dominator instead of a single Onslaught with OP tied up in ARU.