To find all "official" Secrets on map E1M2, Nuclear Plant:

In most Doom games that include this map, there are 6 areas
that will affect a player's "Secrets found" score.  (Sony
PlayStation Doom and Sega Saturn Doom add one extra Secret
along a stair-step leading down to an outdoor area.)

When you first arrive on this level, you'll be at the south
end of a large room near the middle of the map.  You'll be
facing north, looking towards a large structure that fills
the center of this room.
Head to the outer wall of the right side of this structure
(the outer east-side wall of the structure), and look for a
hidden wall panel, and open it to reveal a chamber.

Secret 1: Step inside this chamber and Activate the switch
you'll find there.

Turn and step back out into the large room.  Walk southeast
(ahead and to the right) a few paces, to a door you'll find
in the corner.  Open it and head up the stairs, all the way
to the top.
Look for the red keycard on the floor, in the west side of
a small room at the top of the stairs, and grab it.
Leave this room and go left (north), down the stairs, and
look for a tall opening in the corner which leads outside.

Secret 2: Step through the opening, go down the low steps
outside, and onto the grass.  (Note: The Sony PlayStation
and Sega Saturn Doom games will count this as two Secrets
discovered.)

When you're done outside, step back up through the tall
opening in the building, and head right (west) down the
stairs to the door at the bottom.
Go through that door to re-enter the large room you were in
when you first appeared on this map.
Head to the opposite side (the west end) of the room, and
look for a red-keyed door there.
Head west through this door, and take a right, down a short
curved passage that leads to a small slime-floored room.
Look for a pillar in the center of this room and Activate
the switch on its back side.
Leave this slime-floored room, and as you head back towards
the red-keyed door, you'll see a newly-opened wall section
ahead of you, located just south of the red-keyed door.
Walk into this new passage, down a few steps, and turn
right.
Walk a couple paces forward and you'll see a wall edge, or
partition, up ahead of you and a little to the left.
To the right of this partition is a single passage that
continues off to the right: Ignore that path for now.
Instead, walk to the first opening just to the left of that
partition, and continue on in that direction, staying close
to the right-hand wall.
Continue forward (west) and up ahead you'll see a barrel in
the corner.  Walk up to this barrel and turn left (south).
You'll see a green armor jacket ahead of you on the floor
against the wall.  The wall panel right next to the armor
is a secret door.
In SNES Doom, this panel can be opened like any regular
door.  In all other Doom games, use your fist, pistol,
shotgun or chaingun to attack the panel, and it will open.

Secret 3: Enter this newly opened passage.

Follow the winding stairway up to a windowed area where
you'll see the chain saw on a pedestal.  A switch in the
corner of this room will cause the pedestal to lower,
allowing you access to the chain saw.
Go back to the top of the winding stairway, and turn to
face south, so you're looking down the steps.  On the
second landing down from here, search the east wall for a
secret panel, and open it to reveal a chamber.  On your
Automap, this chamber's location will look something like
this:

  | |\___/
  | |____ _
  |____  |_| <- Secret
    ___| |
   |  ___|
  |  |
  | |
  | |

(Note: In SNES Doom this image may be rotated to some other
orientation.)

Secret 4: Step into this small chamber to pick up the armor
helmets you'll find there.

Head back down the steps and step out through the opening
at the bottom of the winding passage.
Turn right (south), and follow the right-hand wall south
and east for a long distance, passing other passages and
openings on your left.
You will come to the southeast corner of this dark winding
maze.  Nearby to the north, you'll find a pair of vertical
metallic strips running floor to ceiling up the east wall.
Between these metallic strips is a secret panel; Open it to
reveal a small chamber.

Secret 5: Step into this chamber.

Turn around and step out of this chamber, and turn right to
face north.
Follow the right-hand wall continuously as it winds north
and west.  Eventually you'll emerge from the dark maze to
find the red-keyed door on your right.
Turn your back to the red-keyed door and you'll be facing
west.  You'll see some stairs ahead in the distance; Go on
up, and you'll come to a slime-floored room at the top.
A winding path leads across this room to a short hallway to
the north.  At the far end of this hallway is an elevator
leading down; don't step on it yet.
Just a few paces before the elevator, search the left-hand
(west) wall of this short hallway for a secret panel, and
open it to reveal a small curving passageway.

Secret 6: Step into this dark passageway.  (You can follow
it down to a raised shelf-like area in the larger chamber
below.)

In the chamber below, Activate the switch on the north wall
to open a passage that leads down to the exit chamber.

Done!

PC Doom players can access a demo of this level that shows
how to find all "official" Secrets, by clicking here.