Ideas:
Beam Overcharger - Small size. Increases energy weapon range & damage by 25%, doubles flux cost.
Police Upgrade - Small size. Increases burn by 1, tactical speed by 10% and sensor strength by 75. Doubles signature profile of the ship using it.
Smuggler Upgrade - Small size. Reduces burn by 2, reduces ship signature by 90%.
Crew Armory - Small size. Allows ship crew to act as 1/2 strength marines in appropriate situations.
Phasing Crystals - Small size. 10% of beam damage bypasses enemy shields unless they are Hardened. Range drops by 25% and flux cost goes up 25%.
LF-EM Generator - Medium sized. Messes with positronic brains, reducing enemy weapon range and speed by 25% each. Only affects AI controlled ships (Probes, Remnant, and any other ships with zero crew requirement).
EM Masking System - Small size. Removes ship from in-game calculations of fleet size when determining whether it is possible to simply avoid/flee a battle or not.
Holographic Projector - Small size. Makes a ship count as double when in-game enemies are deciding whether to shadow, pursue or flee from your fleet.
Sloped Armor - Medium sized. Increases armor deflection rating by 20% (95% is still the limit, of course).
Nanotech Armor - Medium sized. Rare blueprint discovery required. Ship armor heals itself 1 point per second and fully heals 100% at the end of a battle at no supply cost. Massive power requirements reduce ship burn by 1 and tactical speed by 10%. Doesn't work on hull (too complicated for nanites to figure out).
Warp Overdriver - Medium sized. Burn automatically set to 10, regardless of ship size and overriding all other burn penalties. Supply cost increases 10% and fuel cost increases 25%.
Flux-sink Armor - Very small size. Maximum flux is increased by ship's armor rating (and goes down as armor is damaged). Supply cost for CR recover from damage increased by 25%.
AI Targeting System - Small size. Rare blueprint discovery required. All non-missile weapons get +25% leading accuracy, +20% to velocity and +10% to ROF. This hullmod is considered an AI, however, and thus any ship using the mod will be flagged as illegal by any faction that forbids AI (i.e. everyone except TriTachyon) and immediately attacked when scanned by system authorities.
Short-wave Scrambler - Small size. Any guided missiles targeting the ship have a base 50% chance to lose guidance when they come within 750m. Countered by ECCM and doesn't take up weapon slots. Unguided missiles can still hit, of course, especially if they're fast and you're slow.
Special Systems Booster - Medium sized. Increases recharge rate of whatever special, ship-specific mod is present (phase skimmer, afterburners, high energy focus, etc) by 100%. Permanently reduces maximum flux by 500/1000/1500/2000.
Tactical Scanners - Very small, used only in tactical combat. Triples FOW removal range in a 60 degree cone from the front of the ship.
Bypass Module - Very small, used only in tactical combat. Capture points now taken in only 1/3rd the normal time.
Fighter Ops Center - Medium sized, doubles OP cost of all fighters but also doubles their range and increases their speed, manueverability and leading accuracy by 10%.
Orca Refinery System - Massive size, converts ten units of ore into ten units of refined metals per day.
Nomad Refinery System - Massive size, converts ten units of gas into ten units of fuel per day.
Bedouin Autofactory - Massive size, converts five units of organics into five units of supplies per day.
Medical Bay - Medium size, reduces all crew and marines losses by 25% in all situations.
Hospital Module - Massive size, Medium sized, reduces all crew and marines losses by 50% in all situations.
External Cargo Pods - Large size, Increases cargo capacity by 50%, reduces burn by 2.
Cloaking Device - Rare blueprint discovery required. Small size, reduces sensor range by 20%, burn by 1 and signature by 100% when "going dark" is active. Does not count towards ship limit when determining if fleet can avoid battle or not (same as holographic mask). If all ships in a fleet are carrying this while "going dark" is active then ID cannot be determined by enemy patrols (no rep loss for transponder or contraband - dialog is bypassed, skips straight to "leave").
AI Hivemind - Rare blueprint discovery required. Medium size. Illegal in the same way as AI Targeting System. Only affects drone fighters. For every ship equipped with this in tactical combat, all drone fighters have their range, speed, target leading and damage increased by 5% (up to 100%).
Military Reconfiguration - Negative OP cost. Ship loses 80% of cargo capacity and gains 1 OP per 10 space sacrificed. Requires "militarized subsystems" as a prerequisite. CR recovery cost from combat also increases by 10%.
Luxury Berths - Medium size. Reduces crew, marine and officer monthly expense by 25%.
Recycling System - Medium size. Reduces monthly supply cost by 25%.
C-Extender - Small size. Reduces burn by 2, tactical speed by 10% and fuel costs by 35%. Incompatible with other burn speed affecting hullmods.
Interceptor Package - Small size. In tactical combat, speed is increased by 25% and CR decay rate by 50%. Does not affect maneuverability.
Backup Systems - Small size. Increases CR recovery speed from combat by 50% and minimum crew by 20%. Does not effect supply cost (still costs as much as normal, it just happens faster). Does not effect actual battle damage. In combat reduces time to get offline systems back online by 10%, similar to "damage control" (but not as good).
Comms Hacker - Small size. Hacks into enemy comm systems and plays "Flight of the Valkyries" as you engage them, doubling their morale loss whenever that particular ship scores a kill and thus increasing the odds that enemies will flee combat when damaged or outnumbered. (<-- I know this is just silly but I couldn't resist adding it in there)
