When you go to flip the switch that drops the barrier raised on grabbing the yellow keycard, there is a portion on the northern side of the stone wall to the west with thicker holes in it than the others. Open this wall to find a plasma gun and (on I'm Too Young to Die and Hey, Not Too Rough only) a computer map (sector 107). This can also be accessed from secret #2.
After flipping the switch to lower the barrier, head into the huge corridor to the west of the yellow keycard room and take the elevator up to the alcove with the blue armor. Press on the wall right south of the elevator to activate a slow lift (sector 188) containing four boxes of rockets. This lift leads directly to secret #1.
In the room that opens the way to the grassy area with the lava river, open the wall with the lightning bolt on it to the south to find a backpack and a soul sphere (sector 285).
Inside the eastern room of the wooden house is a portrait on the eastern wall and an armchair in the southwest. Climb on the armchair and fire at the portrait (try using the super shotgun) to reveal a secret compartment (sector 226) containing a megasphere.
On the first time you try to get to the exit, you will be teleported to the first room in the level, in front of a wall opening to reveal a very long flight of stairs. Climb all the way down these stairs to find a toxic pit with a platform (sector 368) on the other end holding a blue armor, a megasphere and (on Hurt Me Plenty or above only) a computer map.
Lower the eastern wall in secret #5 to reveal a radiation suit (sector 369).
Getting onto the platform in secret #5 will cause a wall in the south of the toxic pit to lower, revealing a sewage system. In the west is a tunnel leading to a room with a switch lowering the barrier blocking the level exit. Head down the sewage tunnel until you come across a portion of the western wall with filth originating from the ceiling. Open this to reveal a stairway to the platform (sector 381) from where the imps attack you in the switch room, containing three energy cells and a soul sphere.
Sector 323 is a teleporter that leads to the outdoor section south of the start, on the walkway from which the exit is accessed. It is supposed to be accessible after you climb the stairs to secret #7, and starts with its floor raised to its ceiling. However, linedef 2432 is set as type 40, which raises the teleporter's ceiling to the height of the highest adjacent ceiling, instead of a floor-lowering type of any kind. This means the teleporter cannot be used, and you must backtrack all the way over to the walkway to access the exit.