E1M1 Contains 11 secrets and a super secret.

Secret1 : When you first start the level and leap out of the sarcophagus you will see two more on either side of you. Turn to the one on the right, duck and press the side of it. It will lower and allow you access to a small chamber behind it.
Contains : A box of flares

Secret2 : Also in the first room, you will see a round structure up ahead of you, press it and it will rotate to reveal that it is in fact hollow.
Contains : A box of TNT

Secret3 : When you exit your tomb in the beginning i.e. go outside, if you turn to the hedges on your right when you exit the building and press them, a section will lower to reveal a hidden area. There are two clues to this, firstly, you'll be able to see some soily footprints on the grass leading to the secret and a section of the hedge will appear more pale than the rest, this is the one to press.
Contains : Body armour

Secret4 : When you reach the graveyard outside the Morningside funeral home, you'll be able to see an object on top of the grey tomb-like structure on the right of the room. Leap onto a tombstone and then leap onto the gate and then move to the top of the building and collect your prize.
Contains : Guns-akimbo

Secret5 : When you are in the main room of the Morningside funeral home you'll see two pews. Stand on the seat of the front pew and you'll hear a stone sliding sound. The stage at the back of the room has slid forward and revealed some fiends as well as a prize.
Contains : A box of flares

Secret6 : When you move through the curtains through the right of the main room, you'll see an organ in front of you. Play it by pressing your use key. You'll be rewarded with music and a small panel will slide open on top of the organ.
Contains : Beast Vision

Secret7 : If you turn right at the organ and proceed down the dark passage to the morgue section of the building. You'll see that one of the body containment cells has a crack on. Use explosives to blow it up. Crawl inside.
Contains : Body armour

Secret8 : If you continue down the morgue passage and enter the crematorium, you'll see a bloody saw on the wall in front of you. Press the saw and you'll see it slide downwards. The panel which held all the bottles to the left of the saw has slid away and has revealed a secret room.
Contains : 2 boxes of flares

Secret9 : In the crematorium you'll see a conveyor belt leading to a fire. You must be brave and enter the flames.
Contains : Life seed

Secret10 : When you exit the crematorium and turn right and then go right from there, you'll find another crack on one of the body containment cells, use explosives on the crack and jump and crawl inside. The crack will be in the dark unless you turned on the light, which flickers anyway. You'll have to look at the top row of the cells.
Contains : Fire armour

Secret11 : When you've passed through the grey stone doors which require the dagger key at the end of the passage and turn to your right, there will be a sarcophagus in the room which has its lid pushed up against the wall. Jump into the small space behind the lid.
Contains : A box of flares

Super Secret - This is in the final room of the level, the top half of the wall which you see on the right on this picture is fake. You can walk through the top half of the wall and enter the secret chamber. The problem is that you can't jump high enough to reach the secret chamber, so it would be wisest to lure the zombie in the previous room down into this area and then jump on his head and then leap into this hole. This secret can't be seen on the map either, so this is a real tricky one, but the rewards more than justify the efforts.
Contains : Napalm launcher

E1M2 Contains 8 Secrets.

Secret1 : When you enter the waiting area of the station. You'll hear a telephone ringing. Press the telephone second from the right and it will slide down. Revealing a secret space.
Contains : Basic armour

Secret2 : When you enter the kitchen area of the bar (Cask of Amontillado Pub & Grill), blow up the fire hydrant on the opposite wall when you enter. A secret room will be revealed.
Contains : A box of flares and a box of TNT

Secret3 : In the same kitchen area, if you open the cupboard and Caleb says: "The leftovers." Press the odd piece of wall with the bloody handprints on. It is in fact a button which opens a wall in the secret area you find once you've blown up the fire hydrant (see above).
Contains : Limited invisibility

Secret4 : When you enter the library like place (Pickman's rare books and maps), press the cash register. Up ahead of you a bookshelf will lower.
Contains : Doctor's bag

Secret5 : When you enter the library like place (Pickman's rare books and maps), press the cash register. To the right of you a bookshelf will have lowered.
Contains : Body armour

Secret6 : When you are in the passage leading to the door that requires the moon key (the one with the strange fading light), smash one of the windows and step onto the window ledge outside.
Contains : Life seed

Secret7 : When you open the moon key door. Up ahead of you will be a painting of a woman. Press the painting and it opens.
Contains : Guns akimbo

Secret8 : In the final section of the train station, where the train arrives, there is a small wooden door leading to a small storage area with tools and boxes inside. There is a crack on the righthand side of the wall facing you when you enter. Use explosives on the crack and a secret passage is revealed.
Contains : A box of shotgun shells and a box of TNT

E1M3 Contains 6 Secrets and a super secret.

Secret1 : When you open the door to access the storage compartment of the train, move to the opposite side of the chamber. Move straight to the box situated there and jump on. Turn around and waiting on a nearby box for you is a gift.
Contains : Life seed

Secret2 : In the storage compartment of the train you'll notice a blue chest like structure. Open it.
Contains : Beast vision

Secret3 : When you are in the large dining area with all the cultists and the skull key, there will be switches under the counters of both bar areas. Press the switch and the curtains open and close, but a small panel opens on the nearby wall too.
Contains : Reflective shots

Secret4 : When you enter the kitchen area of the train. There will be a stove/cupboard like object on the right hand side of the cooking flesh on the heated area. Open it.
Contains : Flare pistol

Secret5 : When you enter the original carriage that you came through i.e. the first one, if you're carrying the fire key the doors will open and cultists will attack you. In the second room with the cultists there is a crack on the right hand wall. Use explosives on it and you'll be allowed to access a roof area of the train.
Contains : A box of flares, a tommy gun and two bundles of TNT

Secret6 : When you are in the engine room or locomotive of the train, there will be a furnace structure. Open the metal grates on the sides of it and jump inside the fire. There will goodies hidden inside, but you better collect them quickly!
Contains : A flare pistol, a sawed-off shotgun, a tommy gun and a life seed

Super secret - Yeah, so I had to cheat to take this picture, but it's just to show you what to look for. Now, there are three metal compartments that join the train together. The very first one you enter is the one you're looking for. Break the window on the left of the compartment and jump out of the train! Now it's advisable that you keep jumping or, use the god mode cheat just to look for the exact spot and then load, so you know where to look. Now as you can see, there is an open panel. You have to push under the "666" and it will open, allowing you in. I have done it before without losing any health, so it isn't as tricky as it sounds. Oh and some enemies board the train if you find this secret, so brace yourself for attack when you exit the secret. Luckily, you don't have to go back the way you came in!
Contains : A sawed-off shotgun, a tommy gun, super armour, life seed and guns akimbo

E1M4 Contains 12 secrets and the path to the secret level!

Secret1 : When you start the level in the train wreck, stick to the left wall and keep walking. You'll eventually find some flames blocking an area. Walk through the flames.
Contains : Body armour, two bundles of TNT and a box of shotgun shells

Secret2 : The first body of water you reach in the level with the bridge crossing over has goods hiding in it. Dive into the water and swim to the area with all the elevated soil. Surface and you'll see the goods.
Contains : A flare pistol, a sawed-off shotgun, a tommy gun and guns akimbo

Secret3 : When you pass the guy who asks for tickets, if you play the first game on your left (the one with the ducks and smiley faces sliding around) and destroy the offending objects your prize rises onto the counter.
Contains : Life seed

Secret4 : Between the game with the sliding ducks and the kick the head game there is a wall. You can either jump on the mime and jump over the wall, or use the jumping boots to reach the other side.
Contains : Beast vision

Secret5 : It's hard to miss the kick the head game. I would recommend saving and then trying to get those zombie heads into the mouth. If all three make it into the mouth you get a prize inside the mouth.
Contains : DEATH MASK

Secret6 : When you enter the area with the ratburgers on your right, if you look left you'll see a game with a shotgun that you need to destroy the bottles with. To the left of the game there is a wall. You can either jump out of the manager's office window, jump off an enemy's head or use your jumping boots to reach the other side.
Contains : Full drum of bullets

Secret7 : Play the game where you get the shotgun and you need to break the bottles. If you break the three front bottles you get a prize on the counter.
Contains : Limited invisibility

Secret8 : When you're passing through the freak show (where you hear the 'one of us, one of us' sound), you'll see a cage with a zombie hanging inside. Destroy the bars using explosives and poke or shoot the zombie. A panel will open in the wall behind you.
Contains : Guns akimbo

Secret9 : In Jo-Jo's room, with the tight rope. You'll see two warning signs on the front of the pit of snakes. Push the one on the left and an area will open behind the pit of snakes. Inside there are goods and a surprise character...
Contains : 2 boxes of flares and a box of shotgun shells

Secret10 : When you're in the ticket booth where you get the eye key, there will be a stack of boxes. Push the boxes.
Contains : A box of flares and a doctor's bag

Secret11 : When you're in the storage area, with all the boxes and stuff, when you enter, if you turn left and walk to the furthest wall and turn right you should see some damaged boxes. Push them and a box will lower, allowing you access to a secret area that holds a pleasant surprise. (This is the storage area that opens once you get the eye key in the ticket booth)
Contains : Life seed

Secret12 : This picture depicts the bridge which has been destroyed when you move through the moon key. There is a crack on the opposite side of the bridge, so use explosives to destroy the wall. Then you have to jump along the wooden posts sticking out of the water and try to reach the other side. This may take some time, but the rewards are worth it. There is a pool of water on the other side, move through the water and surface on the opposite side.
Contains : Life seed and super armour

Secret level - When you access the secret above, there will be a stone slab with three skulls on. You have to enter a combination code. The combination is Dagger - Eye - Moon. If you're wondering how one's supposed to know this, then listen up. This is the order in which you collect the keys in the level! Also, in Jo-Jo's pad there is a banner on the wall with a dagger, an eye and a moon on. Thanks to my observant friend Cruaich for spotting that one!

E1M5 Contains 9 secrets and a super secret.

Secret1 : When you enter the first hallway with the green tiles on the floor. If you look on your upper left when you first enter the room there will be a platform with some pictures on. Destroy the pictures with explosives and there will be a small secret room behind the left one. You need to use your jumping boots to reach it, though.
Contains : Doctor's bag

Secret2 : When you collect the skull key and all the zombies attack you, once you've killed the zombies there will be a pair of jumping boots where the zombies came out of. Collect the boots and then activate them and jump up. There is a hidden ledge high in the room where the zombies were.
Contains : Reflective shots

Secret3 : When you've pulled the underwater switch to allow you access to the area where Tchernobog shows you which door is the correct one, wait a while after you've pulled the switch. A panel will open on your right hand side if you're facing the switch. Follow the secret passage and surface where you find the water. A hidden room is there.
Contains : Life seed

Secret4 : In the room which has the metal gate where you find the moon key, one of the posters on the wall has a reddish hue to it. Press it, there is a switch hidden behind it. The pillars will lower and a prize will be on the middle one.
Contains : Super armour

Secret5 : Once you've entered the area after the skull key door. If you look out of the windows at the outside area and then look to your left you'll see a metal plated piece of wall. Push it and it will lower, allowing you access to a secret area.
Contains : Limited invisibility

Secret6 : When you are in the cellar area with the barrels on the shelves, one of the ways to access the cellar is via an elevator. If you face the wall while riding the elevator, you'll notice a small chamber on the side.
Contains : Basic armour

Secret7 : In the grand hallway, which leads to the small outside area with the colorful windows, there is a small open space in one of the corners. Activate your jumping boots and leap up there. You can see the gargoyle statue in there.
Contains : DEATH MASK

Secret8 : In the small outside area with the colorful windows there is a raised piece of ground surrounding it. Use your jumping boots toget on top of the raised area.
Contains : A box of flares and a box of shotgun shells

Secret9 : When you're walking down the passage in the grand hall with the two higher pieces of ground on either side of you, shoot the symbol with the eye inside, which is above the door. A panel will open behind the door.
Contains : Guns akimbo

Super secret - This is in the final room of the level, where the bridge crosses over the pit. If you look down and left you'll see a ledge (you may have to put up your gamma to see it, as it is very dark). The ledge is tainted with dark energies which will rapidly drain your life force if you stand on it. I recommend you get the invulnerability before you attempt to get this secret! Land on the ledge and push the wall all over. It will open at a point.
Contains : Life seed and super armour

E1M6 Contains 6 secrets and a super secret.

Secret1 : In the very beginning of the level, when you get ambushed by the zombies, if you look at the opposite wall to the one they break out of, the wall will appear abnormally dark. It is in fact a path. Walk into the darkness and you'll find a stash.
Contains : 5 bundles of TNT and 4 shotgun shells

Secret2 : When you're underwater and enter the room with all the pillars, turn to your right. There will be an underwater passage, move through it and surface at the end. There is a secret chamber.
Contains : Limited invisibility

Secret3 : Just before you cross the bridge to hit the switch which accesses the large doors, there is a corner with two boxes of TNT. On the right hand side of this tiny corner there is a brownish texture with people on. Press it and it opens to reveal a secret area.
Contains : Doctor's bag

Secret4 : Similar to the secret above, before the staircase just before you enter the room with the reflective shots on the far side, there will be a brownish texture with people on. Press it and it opens to reveal a secret area.
Contains : A box of shotgun shells

Secret5 : Inside the room where you get the fire key, there is a large rotating structure on the opposite side of the chamber that cultists attack you out of. If you step into the rotating object and look up on the opposite side of the central post, there will be a switch. Stab it with your pitchfork and the structure will rotate again and attach to a secret area.
Contains : Napalm launcher, 2 boxes of flares, 6 bundles of TNT and a life seed

Secret6 : In the final room with the rotating walls, if you follow the walls i.e. move with them, you'll find a portal. Step into it and you'll teleport to a secret room.
Contains : DEATH MASK

Super secret - This picture is taken in the room where you pick up the moon key. I'm busy looking over the edge and as you can see, something doesn't look right. The clouds are blocking a piece of the wall and a part of the clouds appear higher than the rest. You can make out a rectangular shape nearest to the ledge. This is in fact a ledge you can fall onto. If you fall onto the ledge and walk along it, you'll find a door you can open to access the super secret room. Delicious!
Contains : Flare pistol, sawed-off shotgun, tommy gun, napalm launcher, guns akimbo, super armour, life seed, doctor's bag, limited invisibility and a DEATH MASK

E1M7 Contains 3 secrets.

Secret1 : If you go up the left path, from the start, you'll eventually find a window on your left. Fall out of the window onto the ledge. You can use the teleporter to get back up.
Contains : Super armour

Secret2 : If you go up the right path, from the start, you'll eventually find a window on your right. Fall out of the window onto the ledge. You can use the teleporter to get back up.
Contains : Life seed and a doctor's bag

Secret3 : If you use the jumping boots to leap onto the platform where Cheogh attacks from there is a stash on your right.
Contains : Guns akimbo, a box of shotgun shells and a full drum of bullets

E1M8 Contains 5 secrets.

Secret1 : When you begin the level and exit through the metal gate, you'll notice that there is a forest setting. If you step out of the metal gate and walk straight towards the forest area on the opposite side of the chamber and don't stop walking you'll walk into a secret area you could not see. This is a masked wall.
Contains : A tommy gun and a full drum of bullets

Secret2 : When you're in the room where you first hop onto the river ride of terror, press the large blue sign that reads : "The river ride of TERROR. Caution - you may get wet!" A wall will open on your right.
Contains : Super armour

Secret3 : You'll find two graveyards when you're travelling along the passage with the fleshy walls once you've gone through the skull key door. The last graveyard you find with the pool of green sludge in the corner has a tombstone with a skull on. The tombstone is a much darker shade of grey than the rest of them. Press it and a wall panel opens.
Contains : Life seed

Secret4 : When you first enter the storage room with all the boxes, you'll see boxes in front of you with very thin strips of wood on them. Press the back box and they will both lower to reveal a gift.
Contains : Guns akimbo

Secret5 : When you're outside where all the TNT barrels are, just after you've destroyed the wooden beams nailed in the shape of an X, there will be a wall on your left. Run along the wall until you reach the end of it. Then jump and move forward. You'll land in a secret room. The wall is masked.
Contains : A doctor's bag and six bundles of dynamite