In the courtyard outside — As soon as you get outside, climb up the stairs and run behind the temple you came out of. Collect the armor. Reward: Armor +50.
At the pond — There's a place you can't get to at the pond area with some columns in front of it. Go to the right hand side. Jump around onto the window, and duck to get through. (Alternate path: Go to the left hand side onto some stairs. Sprint them up and jump for the window there. The secret on the right side still needs to be triggered though.) There's the developers as bigheads here and a health pack. Reward: Easter egg, Health +100. Message: "Secret Hall of Developers found!"
The Dark Bride — There are two portables behind a lockup. The portable on the right has a destructible door. Reward: Electricity +50. Message: "Secret found!"
The Dark Bride — To the right of the exit gate for this area, there's a shed with a health pickup in it. If you climb onto the boxes beside it, you can pick up the secret keys. They're used after the second locked door, where you're facing another door — "No Entry" — walk through it and collect the armor. Reward: Armor +100. Messages: "Secret keys found!"; "Secret found!"
At the minigun fight — You need the key from secret 4. At the end of the path is a door you can now walk through and collect ammo. Reward: Minigun Bullets +500. Message: "Secret found!"
Before the courtyard with the Aurigan Cave Demons — When you get to the portable where you pick up the keys there's a Scrapjack on the far wall. To his left (your right)(indoors) is a wall with a slightly darker texture. This wall can be destroyed. Reward: Rockets +15. Message: "Secret Found!"
At the Cloned Soldier fight — There's a portable in this area with a health pickup on it. Jump on some rubble then jump towards it. Reward: Health +50. Message: "Secret found!"
The final battle — On the right side of the entrance is some ammo. Reward: Cannonballs +4. Message: "Secret found!"
The final battle — On the left side of the entrance, behind a tumbled stone, is some armor. Reward: Armor +10. Message: "Secret found!"
The final battle — On the left side of the exit is some ammo. Reward: Devastator Shells +20. Message: "Secret found!"