CMP-150 (SMG 2) - Sewer Retrieval
Combat Sheild (Shield 1) - Trinity Infiltration
DEF-12 Shotgun (Close Combat 2) - Nightclub Stakeout
DW-P5 (SMG 2) - Nightclub Stakeout
FAC-16 (Assault 2) - Trinity Escape (off dead ally)
Falcon (Pistol 1) - Nightclub Stakeout
Frag Grenade (Thrown 1*5) - Nightclub Stakeout
Hawk Boomerang (Thrown 1) - Rooftops Escape
KSI-74 (Assault 2) - Lab Rescue
Laptop (Assault 2) - Trinity Infiltration
M60 (Heavy 3) - Mansion Infiltration
Magnum (Pistol 1) - Rooftops Escape
Magsec 4 (Pistol 1) - Mansion Infiltration
Multi Mine (Thrown 1*5) - Temple Surveillance
Phychosis Gun (Pistol 1) - Trinity Infiltration
Plasma Rifle (Heavy 3) - Temple Surveillance
RCP-90 (SMG 2) - Jungle Storm
Rocket Launcher (Heavy 3) - Bridge Assult
SuperDragon (Assault 2) - Outpost Rescue
UGL Liberator (SMG 2) - Nightclub Stakeout
Viblade (Close Combat 1) - Mansion Infiltration (red triplaser room)

You must complete the stage with the weapon in Joanna's inventory for it to be unlocked.