Primary Weapons:
Smart Tracker: Decrease Graze chance by 10%/20%/30%
Personal Scanner: Increase sight range and visibility by 1/2/3
Red Dot Sight: Increase Crit and Aim against flanked by 5%/10%/15%
Vital Point Targeter: Adds Deadeye ability and increases Aim by -/5%/10%
Heavy Frame: Increase damage by 20%/25%/30% and decrease mobility by 2
Hangfire Propellant: Increase damage by 1/2/3 and reduce Aim by 5%/10%/15%
Suppressor: Increase Crit and Aim by 15%/20%/25% while not visible
Heat Sink: Grants Suppression/+Demolition/+1 use of Kill Zone
Lightweight Frame: Increase mobility by 1/2/3 and decrease damage by 15%/20%/25%
Recoil Stabilizer: Grants 1/2/3 use(s) of Run and Gun
Progressive Trigger: Grants 1/2/3 use(s) of Rapid Fire
High Cycle Chamber: Increased Aim by 5%/10%/15% and damage by 30%/35%/40%, decrease Crit by 100%
High Caliber Clip: Increase damage by 30%/35%/40%, decrease clip size by 2
External Processor: Increase Hack and Psi 5%/10%/15%
Wildcat Cartridge: Increase Crit damage by 1/2/3
Frontload Magazine: Increase Crit and Hit by 10%/15%/20%, decrease by 10%/15%/20% after each shot
Reserve Magazine: Last shot in magazine has 40%/50%/60% increased Crit and 10%/20%/30% increased Aim
Ammo Synthesizer: Creates 1 ammo round per turn, cannot reload/20% chance to create 2/40% chance to create 2
Dragon Magazine: Gives and replaces any ammo with Dragon Rounds, modify clip size by -1/0/+1
Venom Magazine: Gives and replaces any ammo with Venom Rounds, modify clip size by -1/0/+1
Bluescreen Magazine: Gives and replaces any ammo with Bluescreen Rounds, modify clip size by -1/0/+1
Sentinel Scope: Grants 1/2/3 use(s) of Sentinel Overwatch
Undertaker: Increase Crit damage by 1 per seen enemy, max 3/4/5
Duelist's Stock: Increase damage by 25%/30% when user can see only one enemy and that enemy can see user
Seigebreaker Scope: Increase Crit and Aim against overwatching enemies by 25%/30%/35%
Squad Video Feed: Grants Squadsight/+Long Watch/+Ever Vigilant
Double Tap Targeter: Grants Chain Shot/+1 use of Hail of Bullets/+1 use of Hail of Bullets
Belt Feeder: Grants 1/2/3 use(s) of Saturation Fire
Anti-Material Barrel: Increase Shred and Pierce by 1/2/3
Custom Stock: Increase damage by 1/2/3 regardless of hit or miss
Twitch Trigger: Grants 1/2/3 use(s) of Serial
Maximum Caliber Clip: Increase damage by 100%, max clip size 1/+3 Pierce/+15% Crit on unflankable enemies

Pistol:
Red Dot, Personal Scanner, Suppressor and Wildcat: Same as above
Sidearm Holster: Increase action points by 1, decrease mobility by 6/5/4
Widowmaker: Grants 1/2/3 use(s) of Faceoff
Lawbringer: Grants 1/2/3 use(s) of Fanfire
Wolf's Tooth: 40%/50%/60% chance of gaining 1 action point on use, -/5%/10% Crit
Thunder and Lightning: Increase your pistol damage by 1, Sniper Rifle damage by 80%/90%/100%, unable to reload
Hand of Light: Lightning Hands cooldown reduced to 1 and 0%/5%/10% Crit

Sword:
Parrying Blade: Decrease Melee damage by 4/5/6
Blade Flourish: Reduce enemy's chance to dodge by 10%/20%/30%
Serrated Blade: Increase Crit by 10%/20%/30% and Crit damage by 1
Lightweight Blade: Increase mobility by 1/2/3
Vibroblade: Increase pierce by 1/2/3
Momentum: Increase Crit damage by 1 and Crit by 30%/45%/60% on enemies more than 10 tiles away
Dark Inquisition: Increase Melee damage by 80%/90%/100% while concealed
Long Crusade: Gain 2 armor per Slash for 3/4/5 turns
Big Game Hunter: Increase Crit by 30%/45%/60% and Crit damage by 1 against unflankable enemies
Broken Blade: Increase Shotgun damage by 30%/35%/40% and decrease Sword damage by 30%/35%/40%
Deaths Hand: Reaper now increases damage by 2 after each kill/+1 base damage/+1 base damage
Razor's Edge: Gain 1/2/3 use(s) of Rapid Slash
Zealous Conviction: Gain 1 action point after Slashing an impaired enemy without killing it, increase Aim by 0%/5%/10%

Gremlin:
Trojan Protocol: Increase Hacking by 5/10/15
Shock Protocol: Increase Combat Protocol charges by 1/2/3
Blinding Protocol: Grants 1/2/3 charges of Blinding Protocol, which reduces enemy aim by 50% for 1 turn
Tripwire Protocol: Grants 1/2/3 charges of Tripwire Protocol, which reduces enemey mobility by 4 for 1 turn
Super Capacitor: Gremlin damage increased by 1/2/3
Triage Protocol: Grants 1/2/3 charges of Revival Protocol. Requires the Revival Protocol perk
Satellite Uplink: Grants 1/2/3 charges of Scanning Protocol. Requires the Scanning Protocol perk
Shield Protocol: Aid Protocol now Grants 3/4/5 Shields for 3 turns
Override Protocol: Grants 1/2/3 charges of Override Protocol, which makes an ally immune to 1 attack for 1 turn
Distortion Protocol: Grants 1/2/3 charges of Distortion Protocol, which panics an enemy
Targeting Protocol: Aid now grants 5%/10%/15% Crit and Aim for 1 turn
Mascot Protocol: Grants 1/2/3 charges of Mascot Protocol, which grants 1 ally 1 action point
Mjolnir Protocol: Grants 1/2/3 charges of Capacitor Discharge. Requires the Capacitor Discharge perk
Aegis Protocol: Grants 1/2/3 charges of Aegis Protocol, which grants all nearby allies 6 shields for 4 turns
Bastion Protocol: Heals all allies in a radius of 5 by 1/2/3 per turn
Squad Targeting Protocol: Grants 1/2/3 charges of Squad Targeting Protocol, increasing all nearby ally's Crit and Aim by 15% for 1 turn

Grenade Launcher:
HEAT Munitions: Grenades pierce 1/2/3 armor
Corrosive Shrapnel: Grenades shred 1/2/3 armor
Grenade Launcher Trigger: 5%/10%/15% launching a grenade won't cost an action point
Liquid Explosives: Increase Grenade Crit by 10%/20%/30% and Crit damage by 2
Danger Close Explosives: Increase Grendade radius by 2, damage by 1, reduce range by 60%/50%/40%
Longshot Propellant: Increase Grenade Launcher range by 20%/25%/30%
Air Burst Fuse: Increase Grenade Launcher radius by 0.5/0.75/1.0
Frag Satchel: Increase Frag Grenade Capacity by 1/2/3 per slot
Smoke Satchel: Increase Smoke Greande Capacity by 1/2/3 per slot
Hydra Barrel: Reduce Grenade Launcher radius by 2.5, increase Grenade Capacity by 8/9/10 per slot
Plague Satchel: Increase Gas Grenade Capacity by 1/2/3 per slot
Riot Satchel: Increase Flashbang Grenade Capacity by 1/2/3 per slot
Sapper Satchel: Increase all Grenades in the Grenade slot by 1/2/3
Pyro Satchel: Increase Incendiary Grenade Capacity by 1/2/3 per slot

Psi Amp:
Psionic Projector: Increase Psi Offense by 5/10/15
Aura Amp: Increase Solus radius by 1/2/3
Heavy Elerium: Increase Psi damage by 1/2/3, decrease Aim by 5%/10%/15%
Psionic Inhibitor: Increase Will by 15/30/45
Reanimation Module: Grants 1/2/3 use(s) of Psi Reanimation
Mindblast Module: Upgrades Soulfire to a more powerful version with 3/4/5 charges
Distortion Module: Upgrades Insanity to a more powerful version with 2/3/4 charges
Barrier Module: Grants 3 uses of Barrier, granting 5/6/7 shields for 3 turns
Feedback Module: Grants 1/2/3 use(s) of the Feedback ability, dealing bonus damage proportional to target's Psi Offense
Navigator Module: Grants 1/2/3 use(s) of the Teleport ability
Sympathy Module: Upgrades Inspire to a more powerful version with 2/3/4 charges
Neural Network: Grants a second use of Domination/+Reduces cooldown by 1/+Reduces cooldown by 1
Reality Sink: Upgrades Null Lance to a more power version with 1/2/3 charges
Void Anchor: Upgrades Void Rift to a more power version with 1/2/3 charges

Armor:
Fire Suit: Grants immunity to fire
Poison Suit: Grants immunity to poison
Acid Suit: Grants immunity to Acid
Tactical Sensor: Increase defense by 5%/10%/15% against enemies within 8 tiles
Reactive Sensor: Increase by 5% per visible enemy, up to 15%/20%/25%
Blast Vest: Increase Armor by 1, decrease explosive damage taken by 50%/70%/90%
Hardpoints: Decrease chance to be Crit by 5%/10%/15%
Flexweave: Increase mobilty by 1 and Dodge by -/10%/20%
Undervest: Increase HP by 1/2/3
Mag Deflector: Decrease Mag weapon damage taken by 20%/25%/30%
Energy Diffuser: Decrease Plasma weapon damage taken by 20%/25%/30%
Shield Battery: Grants 1/2/3 use(s) of an ability that grants the user 5 shields for 3 turns
Leg Servos: Grants 1/2/3 use(s) of an ability that grants the user 3 mobility for 1 turn
Digital Camo: Reduces detection radius by 10%/20%/30%
Medivest: Passively heals 2 HP per turn, up to 6/8/10
Rage Stimulant: Increases Aim and Crit by 10%/15%/20% when injured
Medi-Satchel: Increase Medikit capacity by 1/2/3
Smoke Satchel: Increase Smoke Grenade capacity by 1/2/3
Spotter's Satchel: Increase Battle Scanner capacity by 1/2/3
Shock Absorbant Armor: Decrease damage taken within 4 tiles by 30%/35%/40%
Body Shield: Increase defense against nearest enemy by 15%/20%/25%
Stimplant: Grants 1 use of an ability that increases mobility by 3 and armor by 3/4/5 for 1 turn
Reactive Servos: Increases Overwatch Aim by 5%/10%/15% and allows user to fire Primary Weapon back at attacker
Absorption Shield: Any attack that deals more than 25%/30%/35% of the user's HP will be reduced to that amount
Shield Gate: Grants 1/2/3 points of shield, user cannot lose HP while shield is active
Riot Harness: Increases Flashbang capacity by 1 and damage by 1/2/3

<Reserved for Spark Descrptions - I got tired>

Spark Descriptions (Not thorough. I just a quick glance at the script.)

Armor:
NorthStar: -2/-3/-4 cooldown on strike (used to have a 3 turn cool down ...)
Stranglehold: 100% stun 2cd & +20/25/30 defense
Arm Servos: +1/2/3 strike damage

Bits:
Spotter: 2/3/4 rounds marked
Survival: 1/2/3 shields 2turn cd
Repair: +1/2/3 charges of repair
Rocket: 1/2/3 uses
Shredder: 1 use/+2range/+4range
Flamethrower: 1 use/+1width/+2width
Blaster Launcher: 1/2/3 uses
Plasma Blaster: 1/2/3 uses
Nova: +3/4/5 Nova uses
Sacrifice: +1/2/3 Sacrifice uses
Bombard: +1/2/3 Bombard uses
Overdrive: +1/2/3 Overdrive uses
Trojan: +50/70/90 hack

Absolutely wonderful. (belated) thank you for this, I've used it a lot and I felt I ought to comment.

I really wanted to see how OPAF custom stocks would be on pistols, but apparently it's not as simple as adding CanApplyUpgradeToWeaponPistol to the Creation Templates :(

There's at least a few others that don't appear to show up in the list, but I've found them in-game. Such as an item that reloads when you sprint.