This achievement is pretty simple to get, but it can be hard to figure out exactly what you're missing if you don't know the full list. So here it is, complete with where you can find entries.
Contrary to the other solution, it is not necessary to hack any terminal, let alone all of them to obtain this achievement. *I should point out that you still need to access them to open up some areas, but playing the hacking minigame isn't required to advance.*
To obtain the weapon upgrades, you will need to have that weapon to access them.
Imperial Convoys: Available at the start of the game.
Meet With Enemy: Run into a truck on the map to get the entry.
FSA camps: Available at the start, or upon entering area 00, I'm not sure. You'll definitely get this one though.
Areas 00-12: You'll get these as you enter each area.
Areas 13-19: This is actually one entry, and you will get it upon entering any of these areas.
Secret Tunnels: In area 19 there is a POW in the second level door. Hit him a few times with your arm, and he'll tell you about tunnels between areas 15 and 18, and 14 and 17.
Weapon Handling: Available at the start.
Small Health Pick-up: Defeat an enemy while missing some health and he may drop one. They will also appear upon successfully hacking a terminal. (Assuming you're missing life, of course.)
Medium Health Pick-up: Same as above.
Large Health Pick-up: Same as above, except these tend to drop in the later stages.
Score Token: Defeat an enemy for the first time in a stage while at full health, and he will always drop one of these. Pick it up for the entry.
Extra Life: You can easily find one in a meet with the enemy stage, or in the "syringe" doors in neutral areas.
Yashichi: Entry received after obtaining any yashichi.
Revolver: Available at the start.
Revolver Upgrade: Area 00.
Grenades: Clear area 01.
Grenades Upgrade: Area 02. Directly above the boss door is where the upgrade is located. To get there, go under the green doorway with the tank at the top of the stage, and while underneath near the left side of that platform, drop a grenade below you. You'll hear a sound to confirm you've opened the path to the door.
Plasma Rifle: Clear area 04.
Plasma Rifle Upgrade: Area 06. When you get to the part where barrels start rolling at you, head all the way to the right, drop down, and grapple the area just to the left of the light at the end of the platform. Drop down, and you'll find a door. Go in, dispatch the mini-tank droids, activate the switches with the plasma rifle, and enter the newly opened door to find your upgrade.
Bazooka: Clear area 05.
Bazooka Upgrade: Found near the end of the Albatross. Impossible to miss.
Shotgun: Clear area 02.
Shotgun Upgrade: Area 08. When you enter the door at the start of the level, go up 3 floors, and take the path to the right. It'll seem like a dead end, but you'll notice a ledge you can grab above you. Swing off the lower platform and grab it. You'll probably be at a dead stop, so use the shotgun to get yourself moving again. You'll then swing off to the left and grab another ledge above you. Use the shotgun to get moving again, swing over to the door, and find your upgrade inside.
Vector Cannon: Clear area 09.
Vector Cannon Upgrade: Area 10. After you clear the sprinkler droids, you'll come to a shaft with spikes at the bottom. Go up the shaft and to the left, until you start taking fire from more sprinkler droids. Instead of continuing left, go up and to the right. Past the sprinkler cannon(s) you will see a door and two trigger blocks. Hit them both with the vector cannon, and walk in to claim your prize.
Joe's Machine Gun: Found in area 18 after clearing area 07.
Joe's Machine Gun Upgrade: Area 07. Instead of going in the door at the start of the area, fall into the pit at the right. You may die a few times here, but the idea is to grab the ceiling after falling for a short time, and continuing right. Head up, and you'll come to a door with a trigger block. Empty your machine gun into it to open the door and find the upgrade.
Red Comms Chip: Available at the start.
Green Comms Chip: Area 15.
Blue Comms Chip: Area 14.
Yellow Comms Chip: Area 17.
Shin Guards: Clear Area 08.
Bulletproof Vest: Clear Area 11.
Helmet: In the secret tunnel between areas 15 and 18. To access the secret tunnels, find the POW in area 19 and hit him a few times with your arm. The video also shows where to get the secret dossier.
Iron Boots: Area 16.
Health Recovery Pills: Clear area 10.
Permit: Clear area 03.
Flares: Found in Area 13.
Secret Dossier: In the secret tunnel between areas 14 and 17. To access the secret tunnels, find the POW in area 19 and hit him a few times with your arm. Note that if you're on hard or super hard, you will probably need the vector cannon here to set off trigger blocks. On normal or easy, they're not present. Continue through the stage, get to the door at the end, but do NOT enter it. Instead, lower yourself under the platform by dropping a bit, then grabbing on to the platform again. You should be able to spot a rail below you now. Wait until the platform comes below you, and get on it. Take it to the right and find the dossier. The video for the helmet also shows how to get this.
Power Claw: Clear area 06.
Enemies and Hazards
Patrol Soldier: You can't miss this. Just kill a soldier in area 01.
Cover Soldier: Everywhere. You'll encounter quite a few in area 01.
Heavy Weapons Soldier: One is right next to the boss room in area 01.
Shielded Soldiers: There's one near the boss door in area 04.
Bomb Expert: On the way to the platoon boss in area 04.
Close Combat Soldier: Near the beginning of area 04.
Cable Backpack Soldier: You'll have to kill a couple in area 09.
Fly Droid Operator: On the way to the platoon boss in area 04.
Fly Droid: On the way to the platoon boss in area 04. Thrown by fly droid operators.
Barrel Droid: Area 06. Near the end of the stage.
Propeller Droid: Area 05. They'll appear after the first comms room is accessed. These will not appear on easy difficulty.
Mini-Tank Droid: Area 02. They drive the tank droids, but will also appear by themselves in many other areas.
Tank Droid: Area 02. The larger tanks that are driven by mini-tank droids.
Droid Sprinkler Cannon: At the start of area 10. There are a couple in area 5 might work for this as well, but I couldn't be certain as I didn't destroy them on my recent playthrough.
Imperial Sidewinder Motorcycle: These can be found in the meet with the enemy stages zipping in front of the AA truck at the end of the level.
Battery Powered Barrier: There's a couple in the elevator shaft in Area 01.
Central Powered Barrier: You'll get this as soon as you enter area 12 for some reason.
Bear Trap: Area 03.
Blue Rolling Barrel: Area 06. They are pushed by barrel droids.
Slime Blob: Area 02.
Quicksand: Area 03.
Molten Metal: Area 11.
Mechanical Crunchers: You'll find these on the Albatross.
Retracting Blocks: Found earliest in area 00 on the upper level. Grapple one to unlock the entry.
Bosses - you just need to fight them to unlock the entry.
D-1 Beetle: Area 01.
D-1 Beetle v2: Area 06.
Siege Machine: Area 05.
Siege Machine v2: Area 09.
1st Platoon: Area 04.
2nd Platoon: Area 08.
Power Pod: Area 03.
Power Pod v2: Area 10.
Fabricator: Area 02.
Fabricator v2: Area 11.
The Leader's Helicopter: At the end of the Albatross
The Database: Available at the start.
The Imperial Army: Available at the start.
The FSA: Available at the start.
Project Albatross: Available at the start.
Super Joe: Clear area 07.
Gottfried Groeder: Clear area 07.
Haley: Available at the start.
Generalissimo Killt: Clear area 12.
The Leader: Clear area 12.
Air Vent Block: You'll get this in area 05 near the end of the level.
Stone Pillars: At the start of Area 04.
Cracked Wall: There are several places to get these, the easiest of which is probably area 04. Above the comms room is a blue barrel. Up one level and to the left is the cracked wall. Throw a grenade at it and you will get both this entry and the cracked floor entry.
Cracked Floor: See above.
Mechanical Lever: There's plenty in the Albatross, but you'll likely run across one before then.
Trigger Block: You'll see one of these at the top of area 05, and will have to use one to get into area 7.
Bolted Wall: There's one in area 09 near the start. When you dispatch the first pair of backpack cable soldiers, you'll be forced to fall down a shaft. Halfway down, there is a path to the left. Grab the ceiling on the way down, and get in the hallway. There will be another pit to fall down to the left, and at the bottom you'll find the bolted wall.
Blue Barrels: Practically everywhere. There's some at the start of area 01. You must pick it up to get the entry. Hitting one with a rocket or grenade may work as well.
Yellow Barrels: In the gas room inside the Albatross.
Outer Wall 1: At the beginning of area 06.
Outer Wall 2: At the beginning of area 03.
Communication Terminals: Access the terminal in a comms room.
Communicate With HQ: Access the terminal in a comms room.
Hack Enemy Network: Access the terminal in a comms room.
Challenge Simulation Terminal: Enter a challenge room door in any neutral area and access the challenge rooms. This will also unlock the next few entries.
General Challenge Room Rules: See above.
Bullets: See above.
Challenge Rooms Stars: See above.
BC Trailer - Available from the start.
www.bioniccommando.com: Available from the start.
BC Retro Outfit - Available from the start.
BC Prototype Weapon: This one is in the Albatross. Once you get past the gas, mechanical, and electrical areas, you'll go through the door in the main hallway. If you're on hard or super hard, you'll be in an outside area you'll have to complete first. After that, you'll be inside again, in a twisty corridor. Follow the lower level all the way to the right and take the elevator up. There will be electric barriers everywhere. You'll need to use several switches to turn them off. After that's done, you'll head across an area with a few moving platforms, and the floor will be electrified. When you come out at the top area, there will be a switch near the ceiling. Kill the mini-tank droid and the sprinkler cannons, then activate it. From here, you need to backtrack through the area you just came from, and go down to the door. Don't enter it though. Instead, go left through the hallway, and the prototype weapon will be at the end.
Purple Matrix: After collecting all 12 yashichis in areas 01-12, go back to area 00. On the ground level on the right side, there will be a door with the yashichi symbol on it. Enter it, and inside will be the purple matrix.