E6M1 Contains 4 Secrets and a super secret.

Secret1 : When you first enter the shop. Push the cash register. A panel will open behind you.
Contains : Guns akimbo

Secret2 : Through the eye key door there are some cupboards. Push the one at the back of the room and it will slide open to reveal a secret space.
Contains : Basic armour

Secret3 : When you enter the skull key door and pick up the moon key, look at the box. There will be some wooden planks on the box wall instead of the box texture. Push them and they slide awayto reveal a secret space.
Contains : Tommy gun

Secret4 : There is a crack in the wall on the roof. Blow up the crack with explosives and you'll open a secret room.
Contains : Life seed

Super Secret - This is in the store. This is on the left of the room. Make your way onto the shelf and push the wall. It will slide open.
Contains : Life leech

E6M2 Contains 2 secrets.

Secret1 : When you enter the first building with all the boxes and barrels inside and go up the slope to get to the second level, you'll hear a door opening. Go back to the first level and a box will have lowered to reveal a secret chamber.
Contains : Jumping boots

Secret2 : When you begin the level and exit your beginning chamber, there will be Blood writing on the wall that says : "Stay out". This is in fact a masked wall. You can jump through the sign as there is a fake wall behind it, which leads to a secret space.
Contains : Guns akimbo

E6M3 Contains 7 secrets.

Secret1 : When you enter the first room where you have to enter the grate and there's that small vehicle with wheels that the fanatics ride in, there is a box with a red cross on. There is a crack next to it. Use explosives on the crack to open a secret passage.
Contains : Sawed-off shotgun

Secret2 : In the room where you collect the dagger key, there is a bookshelf. Push the bookshelf and it will lower to reveal a secret space.
Contains : 2 Proximity mines

Secret3 : In the room where you collect the dagger key, push the small drawer on the left behind the counter. The back wall will slide away to reveal a secret space.
Contains : Voodoo doll and reflective shots

Secret4 : In the main storage room, below the door with the writing on (manager's office). Look to the left, there will be a high stack of boxes with the 'x' wooden planks on. Push them and they will lower. You need jumping boots to reach the small space it has revealed.
Contains : DEATH MASK

Secret5 : At the far end of the storage chamber there is a crack on the dark grey wall. Blow it open and a secret passage is opened.
Contains : Tesla cannon and basic armour

Secret6 : In the storage room after you've opened the skull key door, there will be a small concealed space in the northeast corner. Access it.
Contains : Guns akimbo

Secret7 : In the room with the conveyor belt-like object in the middle, there are two computer terminals at the right side of it. Push the one on the right and a panel opens behind you.
Contains : Life seed

E6M4 Contains 4 secrets (out of 5! This is sloppy work on monolith's part, they didn't make the fifth secret count towards the secret count. So if you've got four, you've found all the secrets)

Secret1 : When you're swimming around and turning on the giant turbines with the buttons, one of the generator's has a hole, so you can surface inside.
Contains : Super armour

Secret2 : In the main water area, with the rotating structure and all the bridges leading to it, swim around underwater, there will be an underwater passage.
Contains : Life leech and a life seed

Secret3 : When you first enter the watery area with the rotating structure in the center, look to your left. There will be a button. Shoot the button and then look to the structure behind the one behind you with the glass window. A ledge will have presented itself. Hop to it.
Contains : Limited invisibility and guns akimbo

Secret4 : In the sunken ship, the chamber with the spider key inside holds a crack. Blow up the crack to access a secret chamber.
Contains : Tesla cannon

E6M5 Contains 5 secrets and a super secret.

Secret1 : If you go down the passage with the windows on the side (the passage has hell hounds inside), and push the wall with the different texture at the end of the passage, it will slide away to reveal a secret chamber.
Contains : Doctor's bag

Secret2 : In the building with the pillars on the outside, that holds the fire key door, there is a wall which consists of rocks and it has a small space above it. Throw dynamite at it to destroy it. A TNT barrel will present itself. Destroy the barrel and a space will be opened in the wall.
Contains : Fire armour and a bundle of TNT

Secret3 : If you go down the passage with the windows on the side (the passage has hell hounds inside), and blow up the red brick wall, you will find a secret chamber.
Contains : Super armour, a box of shotgun shells and 2 tesla charges

Secret4 : In the chamber with the powerful object in the center, where you get the eye key, there is a ledge nearby, jump onto it. It will become apparent that there was another way of entering this secret.
Contains : Life seed

Secret5 : As you can see in the picture below, there is a hole in the wall of this chamber, if you fall down it and keep moving forward you'll land on a secret ledge.
Contains : Guns akimbo

Super secret : Look at the secret above. When you land on the ledge, turn left and push the wall. It will open to reveal a secret chamber.
Contains : DEATH MASK

E6M6 Contains 10 secrets.

Secret1 : When you first enter the fortress, look at the tower on your left. There is a button on it. Shoot the button and a panel on ground level will open.
Contains : Voodoo doll and reflective shots

Secret2 : Inside the tower on your right, when you first enter the fortress, there is a button. Push it and a panel will on the ground level will open.
Contains : Guns akimbo and a box of flares

Secret3 : When you enter the fortress and take a left turn and pass through the door there will be wooden planks in an 'x' shape on your left. Take a right turn and go to the end of the passage and push the wall, it will lower to reveal a secret space.
Contains : Beast vision and a box of shotgun shells

Secret4 : If you ride the wall which drops to activate secret3, it will take you to a secret ledge.
Contains : 2 basic armours, a gasoline can and 5 remote detonators

Secret5 : If you ride the wall which drops to activate secret3 and push the pillar it will open.
Contains : Fire armour and a life seed

Secret6 : There are quite a few ways to enter this secret, here's one: When you're in the graveyard with the elevator leading to the wooden 'x'. Use your jumping boots to reach the platform where the acolyte was.
Contains : Super armour

Secret7 : When you're in the rooms that joins the the underground lab to the water filled area, there is a button on the wall. Press it and a panel opens.
Contains : Flare pistol and limited invisibility

Secret8 : When you enter the storage room with the bats, jump on top of the boxes and pushthe wall behind them. A panel will open.
Contains : Limited invisibility and a crystal ball

Secret9 : In the graveyard with the severed hands inside, if you move towards the other part of the gardens, pass through the archway and push the right wall of it. It will lower and is in fact an elevator.
Contains : Super armour

Secret10 : Jump into the sacrificial pit surrounded by the Cabal soldiers.
Contains : DEATH MASK

Secret level - Before you enter the moon key door, shoot at the eye symbol above the door (top left of picture) and the door will open as seen in the picture.

E6M7 Contains 3 secrets.

Secret1 : When you enter the area with all the fireballs, one of the blackish walls on the right side of the room is in fact a door.
Contains : Limited invisibility

Secret2 : When you go through the right door in the beginning (the wooden one) and cross the bridge and you are surrounded by the smooth brown walls, push the wall to your left. It will lower to reveal a secret passage.
Contains : 5 sets of 4 shotgun shells and guns akimbo

Secret3 : Push the left skull symbol on the skull key door, a nearby passage opens. This is a 'cheap' secret but the rewards justify the efforts.
Contains : A box of shotgun shells, 2 spray cans, a box of TNT, a full drum of bullets, 3 sets of 4 shotgun shells, 3 sets of a few bullets, a doctor's bag, 2 boxes of flares and a life seed

E6M8 Contains 0 secrets.
How unfortunate.

E6M9 Contains 5 secrets.

Secret1 : When you go around the very first corner, push the wall to your right. It will slide away to reveal a secret spot.
Contains : Flare pistol

Secret2 : When you pick up the skull key, push the switch against the wall and look to the opposite wall, on the other side of the lower chamber. A lift will lower to reveal a prize.
Contains : Life leech

Secret3 : When you go through the skull key door, proceed to the end of the passage and push the far left wall. A lift will lower.
Contains : Life seed and a gasoline can

Secret4 : When you're in the torture chamber, step onto the rack and push the wall behind it.
Contains : Limited invisibility

Secret5 : When you collect the super armour which is near the voodoo doll, push the wall. A teleporter will present itself. If you step into the teleporter it will lead to a ledge. From the ledge you can leap to a nearby secret ledge.
Contains : A box of shotgun shells, a doctor's bag, a trapped soul and 4 proximity mines