Assault Rifle

+10% Damage - Mordin Recruitment Mission – just past merc barricade
+10% Damage - Tali Recruitment Mission – in room blocked by pillar
+10% Damage - Samara Loyalty Mission – on wall in Morinth's apartment
+10% Damage - Zaeed Loyalty Mission (DLC) – Renegade choice only
+10% Damage - Lair of the Shadow Broker Mission (DLC) – delivery
+10% Damage - Illium: Gateway Personal Defense
+10% Damage - Tuchanka: Fortack's Database
+25% Penetration - Unlocked after 2 damage upgrades
Accuracy Improvement - Unlocked after 3 damage upgrades

SMG

+10% Damage - Garrus Recruitment Mission – bypass door near gunship
+10% Damage - Thane Recruitment Mission – just before windy bridge
+10% Damage - Miranda Loyalty Mission – shipping container after first elevator
+10% Damage - Lair of the Shadow Broker Mission (DLC) – delivery
+10% Damage - Citadel: Rodam Expeditions
+10% Damage - Illium: Gateway Personal Defense
+50% Shield Piercing - Unlocked after 2 damage upgrades
+50% Extra Rounds - Unlocked after 3 damage upgrades

Shotgun

+10% Damage - Jack Recruitment Mission – on guard corpse after first large mech
+10% Damage - Grunt Loyalty Mission – awarded automatically
+10% Damage - IFF Mission – in the middle of scion and husk fights
+10% Damage - Lair of the Shadow Broker Mission (DLC) – delivery
+10% Damage - Omega: Kenn's Salvage
+10% Damage - Tuchanka: Fortack's Database
+50% Shield Piercing - Unlocked after 2 damage upgrades
+100% Extra Rounds - Unlocked after 3 damage upgrades

Heavy Pistol

+10% Damage - Tali Recruitment Mission – stairwell bottom at first geth fight (easily missed)
+10% Damage - Thane Loyalty Mission – beginning of 800 wards
+10% Damage - Jacob Loyalty Mission – just past mech destruct barrier
+10% Damage - Lair of the Shadow Broker Mission (DLC) – close after the fire barrier on an research terminal.
+10% Damage - Citadel: Rodam Expeditions
+10% Damage - Tuchanka: Fortack's Database
+50% Armor Piercing - Unlocked after 2 damage upgrades
Critical - Unlocked after 3 damage upgrades

Heavy Weapons

+15% Heavy Weapon Ammo - Freedom's Progress Mission – dead mech outside Veetor's shack
+15% Heavy Weapon Ammo - Mordin Loyalty Mission – terminal just past boss
+15% Heavy Weapon Ammo - Zaeed Loyalty Mission – Near fire extinguisher, Paragon choice only
+15% Heavy Weapon Ammo - Side Mission: N7: Blood Pack Base
+15% Heavy Weapon Ammo - Omega: Kenn's Salvage
+15% Heavy Weapon Ammo - Tuchanka: Ratch's Wares
Weapon: ML-77 - Unlocked after 1 ammo upgrade
Weapon: M-622 - Unlocked after 2 ammo upgrades
Weapon: M-920 - Unlocked after 3 ammo upgrades

Sniper Rifle

+10% Damage - Grunt Recruitment Mission – top of stairs after krogan waves
+10% Damage - Garrus Loyalty Mission – terminal just before raising shutters
+10% Damage - IFF Mission – end of catwalk near sniped husks
+10% Damage - Lair of the Shadow Broker Mission (DLC) – delivery
+10% Damage - Citadel: Rodam Expeditions
+10% Damage - Omega: Omega Market
+50% Armor Piercing - Unlocked after 2 damage upgrades
+50% Headshot Damage - Unlocked after 3 damage upgrades