Inside the lobby, there is a trio of black walls with silver borders. On its southern side is a switch. Press it to find a medikit, security armor, and a super shotgun. (sector 172)
At the east of the storage room, a box of shells and a backpack rest on the south of the control panel. From the northern door, do a strafejump either onto the top of the control panel, after which you can drop onto where the items sit, or onto the place the items are. The secret will be obtained either way. (sector 386) Note that this may take you several tries to pull off, as it is very easy for the sides of the ladder to block you as you try to jump.
In the storage room, walk around the lift, and go to the east. At the end of that corridor is a section of the wall with piping on it. Lower it to find combat armor. (sector 424)
In front of the forklift is a crate, upon which a medikit and a box of ammo sit. After you climb up the first ladder to the blue keycard, turn toward this crate, and jump to it to trigger this secret. (sector 272) Alternatively, you can reach this secret by running across the forklift, climbing up its front and leaping to the crate.
In the room where the red keycard is found, there is a computer with a keyboard. Use it to trigger this secret and receive a computer map. (sector 203)
In the same room, after obtaining the red card, immediately leap east off the desk, and the bookshelf will lower to reveal four rockets and a rocket launcher. (sector 413)
After you trigger the blue switch, there is a set of winding steps that you can climb. This will end in a bridge; drop from the bridge, and into the open crate, to get nine health bonuses. (sector 343)