All items listed here can be obtained during your first time in the zone.
Penguin Cage #1, #2
Shortly into the area, you'll deactivate some laser gates. Head through the left one, and the first two cages will be hanging by a door at the end of the hall.
Penguin Cage #3
Now head through the right laser gate. Grapple to the upper ledge in the next room, then turn around to spot this dangling above the opposite ledge.
Penguin Cage #4, #5
When you enter the large courtyard with several thugs, you'll grapple around some ledges to open the doors in the area. After grappling to the second ledge, turn around to spot a higher ledge above the first one you use. Grapple there to find two more cages.
When you enter a room with a heavy stack of crates in the center, you'll have to crawl through a vent. After battling the shock stick-wielding thug inside, look for a section of the ceiling you can blow through with the Gel Launcher. Up there is a WayneTech crate.
New 52 Gloves
Just beyond room with the stacked crates is a room with lots of thugs and an improvised bomb. The left wall of the lower area has a weak spot; blow it open with the Gel Launcher. Inside this small area is a WayneTech crate.
Penguin Cage #6, #7
When Catwoman sends you to the storage locker, you'll use the Crypto Sequencer on the very next door. In the following room, two cages are hanging: one above, and one to the right.
Penguin Cage #8, #9, #10
After dropping the elevator with the frayed cables, you'll crawl through a vent around some corners. After emerging from the vent and going through the first door, three cages will be hanging high above you.
When you receive the Batclaw, yank open the vent directly to your left. Crawl through to find this in a WayneTech crate.
On your way back to the exercise yard, you'll return to the room where Catwoman first tasked you with reaching the storage locker - it's room with lots of layers where Batman remarked led to the exercise yard. Drop to the lowest floor, then move left to find a vent you can rip open. Crawl through, then grapple up the ledge to find another upgrade inside a WayneTech crate.
Penguin Cage #11, #12
After tearing down the improvised barrier with the Batclaw, you'll crawl through a vent and move in the background. Two cages can be spotted back here before exiting the room.
Penguin Cage #13
This is on the far left side of the very next area.
Penguin Cage #14
This one is very tricky to reach (you may even want to come back once you've obtained the tight rope Line Launcher). Use the Gel Launcher to blow the wooden floor you're standing on, then prepare for a tricky jump. You have to drop through the hole, then immediately glide left. Do this correctly, and you'll reach a ledge where the cage hangs.
Penguin Cage #15, #16, #17
While following the Penguin's blood, you'll come to a room with an electrified pool of water. After clearing this, you'll find three cages hanging from the ceiling in the next room.
While tracing the Penguin's blood, you'll come to a dead end with a large locked door. Before leaving for the Lighthouse, use the Batclaw to pull away a panel in the middle of the room. There's a WayneTech crate behind it.