Once you have entered the eastern teleporter in the start room, look to the north to find a metal grate on a wall. Press on this wall to unveil a staircase leading to a backpack, a bulk cell, a plasma rifle, and a megasphere. (sector 134)
Once you've activated the stairways in the northeast of the blue skull key room, walk up the southwest one, but don't approach the switch. Instead, look to the southwest to find a recess in the wall. Open it to find a corridor leading to combat armor, a soul sphere, and a BFG 9000. (sector 386) If you approach the switch, it will become impossible to access this secret, due to ceilings lowering in the way.