Sixty Feet Under
Clue #1: Circus flyer
After the Solomon Grundy battle, look to the pile of rubble on the right side of the room to find this.
Clue #2: Pile of human bones
When moving through the sewers underneath Industrial, you'll reach three large gates. Use the Shock Batarang to open the one on the right, then move forward. Head past the vent to the bridge, and drop to the sewage flow below. From here, you can use the Line Launcher to reach the other side, where the clue lies.
Clue #3: Plant life
This can be found when searching for the secret entrance to the warden's office. When you crawl through this brick tunnel, look for this white growth. It can be analyzed for a clue.
Bird of Prey
Clue #1: Clipboard
Before entering Cell Blocks proper, you'll grapple across some vantage points. Drop from the second one to find this on the ground.
Clue #2: Small spade
Early in your exploration of Cell Blocks, you'll encounter a shock stick thug inside a vent. Move left through this vent, and use the Crypto Sequencer to open the next room. On the left side of this area are two vent entrances that connect to each other. The clue is inside this crawlspace.
Clue #3: Acetylene torch
On your way to the exercise yard, you'll enter a belfry. Blow the wooden floor with the Gel Launcher, then prepare to drop. As you fall, grapple the first ledge to your right. Crawl through this small space to find a clue on the floor.
Clue #4: Damaged keypad
While following the Penguin's blood trail, you'll come to a freight elevator you need to call. Instead, drop into the small area to find vent you can crawl through. Do so to find a clue atop a machine.
Clue #1: Rubber hose in a pool of fluid
After encountering your first thug wielding a shock stick in Industrial, drop from the yellow edge of the platform. Enter the small vent here, and the clue will be on the ground to your right.
Clue #2: Crowbar
When you return to Industrial, head to the room marked on the map (it's near the Solomon Grundy fight). In here, you can see a pipe leaking spewing sludge. Use the upgraded Gel Launcher to clog the pipe, stopping the sludge and revealing a clue.
Clue #3: Homemade device
When you revisit Industrial, you'll battle thugs atop some electrical flooring. Grapple over the ledge marked with the skull and guns logo, then grapple to the next ledge. Inside this computer room is the final clue.