Accelerated Shields: Can't recall the last time I used this.
Additional Berthing: Put on your people carriers.
Advanced Optics: There aren't many ships/loadouts that would bother with this, so I never see a need to use it.
Advanced Turret Gyros: I occasionally use this, and never remember that I am using it and so can't tell the difference in battle.
Armored Weapon Mounts: I don't know how weapon damage works, and so I never use this.
Augmented Drive Field: I've not played early game for a while and am kinda fine with tugs. I basically never use this.
Automated Repair Unit: Can't recall the last time I used this. But could be good for luddite ships that cripple themselves.
Auxiliary Fuel Tanks: Put on your fuel carriers.
Auxiliary Thrusters: They make onslaughts better but most other ships don't really need them. Good for low tech?
Blast Doors: Crew is a problem for me. I still use Reinforced Bulkheads instead.
Converted Hangar: The de-buffs are so bad on this expensive option that I never use it.
Dedicated Targeting Core: If no ITU then DTU.
ECCM Package: The ITU of missiles. Very fun!
ECM Package: Cool idea, but I almost always end up with the perk that gives me it for free.
Efficiency Overhaul: If you don't want more storage. But I usually go for Surveying Equipment in early-mid game.
Expanded Cargo Holds: Put it on your cargo carriers. Also good for early game nomad/hoarding.
Expanded Deck Crew: I stopped using this at some point so I can't really recall how strong it buffs carriers. I feel.... fine without it?
Expanded Magazines: Does this actually still work? Because it feels like a legacy mod that was never properly updated.
Expanded Missile Racks: Best mod in the game. Fite me irl.
Extended Shields: I think I used this on the Odyssey, and that's it. Never felt too strongly about needing this one.
Flux Coil Adjunct: If you have already maxed out caps, I will occasionally double dip.
Flux Distributor: If you have already maxed out vents, I will occasionally double dip.
Hardened Shields: I like it, but that might be a bad thing as it almost feels TOO good.
Hardened Subsystems: I used to auto include on any destroyer or smaller. But now I play mostly around capitals. CR timers still feel like a bandaid for the AI.
Heavy Armor: Can be nice, but usually I'll play with armoured ships rather then slowing down flimsy ones.
High Resolution Sensors: Good early on.
Insulated Engine Assembly: Surprisingly nice for making your fleet more stealthy, letting pick and choose your fights more often. Also good for protecting onslaught ass.
Integrated Point Defense AI: I love it. But basically never use it for making smalls into PD, but just a PD buff for making fighter flares useless.
Integrated Targeting Unit: I've tried to not need it. But you kinda do.
Makeshift Shield Generator: A good mod, but avoid ships that need it.
Militarized Subsystems: Makes trash, militarized trash. Good enough.
Nav Relay: Get the perk.
Operations Center: I always auto, but never use this. Just seems like a waste.
Recovery Shuttles: I use this! It's all right, does what it says.
Reinforced Bulkheads: Turns fodder ships into lategame reusable fodder. HP is nice.
Resistant Flux Conduits: Feels good in concept, but I have no idea how much it it working for me.
Safety Overrides: I'm too chicken to use this.
Shield Conversion - Front: I've used this on the Odyssey, but over wise haven't found it necessary.
Shield Conversion - Omni: This feels like an outright penalty because the few ships that might want this have such terrible shields anyway.
Solar Shielding: A weird mod but cool enough for the campaign stuff. In battle it seems like the anti-remnant mod.
Stabilized Shields: I think I tried this once. Was it on a conquest? I dunno, basically never use.
Surveying Equipment: Save supplies, and thus save money.
Unstable Injector: Never used this after the nerf.