Clue #1: Wallet photo
This is found just before exiting Industrial. Instead of grappling to the upper ledge, use the Gel Launcher to blow the lower door. Head through and crawl through the maintenance tunnel. When you exit, the clue is on the floor to your left inside the small office.
Clue #2: Tablet computer
When you return with the Batclaw, look for a vent above the main entrance. Rip it away, then grapple up to reach a small room with this inside.
Clue #3: Dental tools
While searching for the secret entrance to the warden's office, you'll explore the sewers in Industrial. When you reach the room pictured above, grapple to the ledge and look to your left. The clue is atop a filing cabinet.
Clue #4: Pile of crumpled papers
The last clue is found in the middle of the Industrial zone, the area with the dual elevators. Grapple atop the left one, then use the Batclaw to rip away the fan across the gap. Use the Line Launcher to zip to newly opened area, and follow the path as it wraps around. The clue is on the ledge you can drop from.
Clue #1: Computer thumb drive
Before grappling to the ledge with the warden's office window in Administration, use the Batclaw to rip away the vent cover to your left. Crawl through here to find a pile of debris that can also be removed with the Batclaw. Underneath is a clue.
Clue #2: Recordable DVD
As you explore the admin basement, you'll reach a room full of pendants (no doubt left by the joker). The clue is atop the overturned lockers in here.
Clue #3: Business card
This clue is tough to reach, so you might want to wait until you've obtained the tight rope Line Launcher. After leaving the admin basement, you'll ascend a series of ledges. The clue is in the top left corner.
Clue #4: Burned paper in trash basket
With the beta Crypto Sequencer in your possession, head to the room pictured above. Open the gate with the sequencer to find a clue inside the small room.