Here is a list of all items found during each mission in the game (If anyone can confirm if those items are random, please tell me). There are many items that you can't find in towns like the Ziege Gun or the Dasler II. Most of the other items can be found either in the city you just came from or in the next one.

Mission 1: None. It's just the prologue.

Mission 2: Raptor Machine Gun,ZOLA 3A Arm

Mission 3: Iguti Type 5 Rifle, Egret R-Launcher (Missile Launcher), PAVOT Arm, CALM Body

Mission 4: ZENITH Legs, Winee Rifle, Rayon EL-002 Computer, Repair S

Mission 5: 2 Repair S, PIZ 8 Missile Launcher, Repair M, HUSKY Mk.III Arm

Mission 6: Empire Rifle, GALVO SV Body, Repair S

Mission 7: Egret R-Launcher (Missile Launcher), FROST Arm, Repair S, GALVO SV Legs

Mission 8: Repair M, Repair S, Sun Owl Missile Launcher, HUSKY Mk.IV Arm

Mission 9: 3 Repair S, WS-14 Shield, 22SN Leosocial Machine Gun

Mission 10: 2 Repair S, 22SN Leosocial Machinegun, GENEM Legs

Mission 11: AVENIR Legs, ZOLA 5A Legs, Argento AGT-44 Computer

Mission 12: In the train: PRISOMEA Body, Erfolg WST-48 Computer, Magic Box Launcher (Missiler Launcher), Repair M, Repair SP. Found with regular enemies: Repair S

Mission 13: 2 Repair S

Mission 14: GROP SP-V Arm, PRISOMEA II Legs, ORCS II Arm, GAROLE II Legs

Mission 15: Veaga VG-15CH Computer, Repair M, Sakata TYPE90 Arm, Sakata TYPE90 Body, Ziege Rifle (AT 1X 99 Hit 99...Whoa!)

Mission 16: ARPEGGIO Body, Repair L, BIZANT II Arm

Mission 17: RATMOUNT Body, ZEROA Arm, Repair L, Verseau RG-04zz Computer

Mission 18: ZINC Arm, Grave II Machine Gun, Smoke Grenade

Mission 19: Slay Missile Launcer, Flash Grenade

Mission 20: ORGEL Body, Verseau RG-04zz Computer, Repair L

Mission 21: Hexafire Mk. II Rifle, Chaff Grenade, Glans AX-1 Computer

Mission 22: FAGOT Body, FAGOT Legs, Repair L, Donkey DX Missile Launcher, Dasler Claw Arm II

Mission 23: Repair L, Wild Goose R-Launcher (Missile Launcher), Sakata TYPE67C Body

Mission 24: Repair L, Winee RR Rifle, BRIZIA II Arm, Karen Device BD-6Kr Computer (FI 98 SH 97 LG 99 AG 99!)

Mission 25: Black Star Machine Gun, Repair S, Paraina Missile Launcher

Mission 26: Artassaut SP Machine Gun, Sakata TYPE103 Legs, Terna RG-0645 Computer, Harpoon Bolt* (AT 1X 99 Hit 97 Range 1-1), Dragon Hand* (AT 1X 99 Hit 98 Range 1-1)

Mission 27: Black Panther Missile Launcher, BRIZIA II Arm, Repair L

Mission 28: Mostro III-SZ Machine Gun, Repair L, Repair SP

Mission 29: 2 Repair L, ELDOS Legs, Donkey DX II Missile Launcher

Final Mission: 4 Repair S

*: The Dragon Hand and Harpoon Bolt are add-ons, they're not Missile Launchers, but they're as destructive as a Ziege Gun. They can be accessed using PAR codes, but if anyone finds a normal way to reach them in Mission 26, you get a Shyster Cookie :P