E3M1 Contains 10 secrets (out of 9!) and a super secret.

Secret1 : In the gallery of arts where you get the spider key, there will be a picture of a woman with a baby. Push the picture and it will open.
Contains : 2 bundles of dynamite and a full drum of bullets

Secret2 : In the grey room where you get the moon key, push the painting at the end of the hallway. It will open.
Contains : Life seed

Secret3 : When you open the moon key door. Enter the room and close the door behind you like a gentleman. Behind the door is a prize.
Contains : Reflective shots

Secret4 : Behind the fire key door there are some chests of drawers. Push the one that doesn't have the bottle on, it will slide open.
Contains : Guns akimbo

Secret5 : In the parlour behind the fire key door, there is a counter with fanatics behind it. There will be a piece of the wall missing. Blow up the hole in the wall, it will give you access to a secret room.
Contains : 2 remote detonators and a proximity mine

Secret6 : When you enter the parlour behind the fire key door, push the right side of the couch next to the flames. It will rotate to reveal a small space.
Contains : Napalm launcher

Secret7 : In the manager's office with the bloated butcher, there is a secret behind the shelves. Push the shelves and a panel will open behind the shelves.
Contains : Limited invisibility

Secret8 : In the room with the dagger key, there will be a matress pushed up against the wall. Push the matress and it will open to reveal an air vent. Break the grate and go through the air vent. There will be a lot and scented trees and a great prize.
Contains : Tesla cannon and two tesla charges

Secret9 : In the room where you get the dagger key, there will be a blown up building outside the window. Jump onto the ruins and explore them.
Contains : Voodoo doll and a proximity mine.

Secret10 : This secret forms part of the super secret. When you attempt to go up the elevator and it explodes a small hole is blown in the wall, if you climb into this hole and keep going upward, you'll find metal plates attached to the wall. Keep climbing and eventually you'll find the hole pictured below.
Contains : Life essence, life seed and super armour

Super secret - See above.

E3M2 Contains 3 secrets.

Secret1 : Before you break the fan so you can fall down into the kitchen area, use explosives on the nearby box that says : 'Danger' on. The box will explode and give access to a secret room.
Contains : Jumping boots

Secret2 : Before you enter the building with the french flag hung above it, one of the pillars gets destroyed. Search the top of the ruin.
Contains : Life seed

Secret3 : Search the room inside the safe with all the cabinets. There will be a button on top of one of the cabinets. There are two ways to reach it. Either you can use your jumping boots, or you can climb onto the damaged cabinets. Along the one wall there is a hidden passage. Just push yourself against the wall on top of the cabinet. When you push the button a nearby room will open. The room is very large, you can't miss it.
Contains : Voodoo doll

E3M3 Contains 5 secrets.

Secret1 : In the very beginning passage, there is a pillar on the left that is gold in colour, instead of grey, push it and it opens.
Contains : Diving suit

Secret2 : When you turn the valves to open the passage, turn the right one once, then again and then a third time (turn it 'on' twice). Turn around and a small panel is open behind you.
Contains : Life seed

Secret3 : When you enter the network of sewers with the green water trailing around everywhere, look to your right. There will be small gold 'boxes' on the wall. Push the one and it opens.
Contains : A tesla cannon and two tesla charges

Secret4 : In the room with the zombies and the straw on the floor, duck and push the table, it will lower to reveal a small space.
Contains : Beast vision

Secret5 : In the room with the cool rotating structure that gives you the eye key, there is a hidden button behind some slime on the computers on the side. A panel will open on your right when you push it.
Contains : Voodoo doll

E3M4 Contains 5 secrets and the path to the secret level!

Secret1 : In the room just beyond the emergency room (the room with the bars looking into the room with all the hanging corpses) there is a painting of a monstrous face. Blow up the painting with explosives and there will be a small hole behind the painting.
Contains : Voodoo doll

Secret2 : In the room with the bed with the curtain surrounding it, there is some machinery against the wall. Push the machinery and it will rotate to reveal a secret compartment.
Contains : Guns akimbo

Secret3 : In the morgue, there are some body containment cells with blood dripping out. Push them and they will slide open.
Contains : Super armour and a voodoo doll

Secret4 : In the morgue, when all the covers blow open, one of the small compartments have a button inside. Press it and then go to the one side of the morgue. There will be a new open area.
Contains : Beast vision

Secret5 : In the syphilis ward, when you look out the window and see the cultists attack the innocents, look on the left wall outside. There will be a button. Shoot the button and the bed next to you will be a lift. The items are all carried by the innocents. Kill the innocents to get the items.
Contains : 4 shotgun shells, a tommy gun, 2 proximity mines, a life essence, super armour, a life seed and 2 tesla charges

Secret level - This picture is taken in the chapel where you get the skull key and the phantasms attack through the curtains. If you look just above my crossair, there is a button that looks like a skull. Shoot the button and a passage behind you will open. The button is just above the doorway when you enter.

E3M5 Contains 4 secrets.

Secret1 : When you're in the room with the spinning ledge holding the fire armour, held by chains, fall into the lava and there will be a teleporter go through it and you'll teleport into a secret chamber.
Contains : DEATH MASK

Secret2 : In the room just before the room with the skull key (with the cultists on the metal ledge) there are two small metal doors against the conveyor belt with the pole with the wires hanging from it. Push the left door and lava will lower behind you, on the opposite side of the chamber.
Contains : Guns akimbo

Secret3 : In the same room as the above, there is a fire on the one side of the conveyor belt. Step into the flames.
Contains : Life seed

Secret4 : In the storage room with all the boxes, when you collect the life seed, turn around and you'll see an object spinning on a box.
Contains : Tesla cannon

E3M6 Contains 5 secrets.

Secret1 : When you enter the starting area, go out the window on the left of the building. Follow the ledge and you'll find the water passing through bars. Nearby there is a ledge. Jump onto it.
Contains : Doctor's bag

Secret2 : In the room that joins to the river, where there are two basic armours nearby and a bridge crossing overhead, check around the room. There will be a small space hidden in the wall.
Contains : Beast vision

Secret3 : On the stairway before you enter the room with the turbines, turn around, a life seed will be in plain view. It is hard to reach with normal jumping, but possible. Jumping boots will work.
Secret4 : In the generator room with the huge turbines, after you've pushed the computer terminals to lower the turbines, jump along them and check behind the front ones when you enter the room.
Contains : Life seed

Secret5 : In the large open water area with the TNT barrels there are spaces in the dam bridge. Scan them.
Contains : A full drum of bullets and a box of shotgun shells.

E3M7 Contains 0 secrets.

How cheap.

E3M8 Contains 6 secrets.

Secret1 : Go to the left wall in the very first room. Push the area between the two torches in the holes in the wall. A panel will open to reveal a secret passage.
Contains : Fire armour, a tesla cannon, a box of TNT and a voodoo doll

Secret2 : When you reach the first wooden doors, turn around. There will be a grey cross. Push it and it will raise to reveal a secret space.
Contains : Limited invisibility

Secret3 : In the greyish room with the green pool in the middle and the gate that needs the skull key to enter, there are details on the wall. One of the details is discoloured, push it and walls behind you will open.
Contains : Tesla charge, a full drum of bullets and 2 proximity mines.

Secret4 : When you collect the life seed in the center of the room with the golden brown brick texture, one of the nearby walls will rotate to release hands that attack you. Enter the part that rotates and stay inside until it rotates. It will turn to face a secret space.
Contains : DEATH MASK

Secret5 : When you collect the eye key and the doors open so that the zombies can attack you, one of the compartments has a red button inside. Push the button and a room will open on the opposite side of the chamber.
Contains : Super armour and 2 tesla charges

Secret6 : In the passage with the light grey walls, before the eye key, there is a crack on the wall. Blow up the crack and there will be a button inside. The button will open a panel on the side of a nearby passage (the roughly oval shaped room), leading to a secret passage.
Contains : Napalm launcher