Directly south of the first room is a concave wall. Open the middle of the wall east of this area to find a plasma rifle. (sector 11) Press the skull on the wall to reopen the door if it closes before you leave.
The door used to access secret #1 also counts as a secret. (sector 12)
The passage to the teleport pad leading outside counts as a secret. (sector 54) It is lined with nine health bonuses.
The teleport pad in secret #3 is also considered a secret. (sector 53) It is thus unreachable, as there is no way to step onto the pad without teleporting away.
The passageway containing the switch which allows access to the yellow key is flagged as a secret. (sector 102)
The space directly in front of said switch is also marked as secret. (sector 101)
The first, unlit space of the passageway to the E room counts as a secret. (sector 127)
The lit portion of the passageway to the E room counts as a secret, too. (sector 128)
The cage from where the imps attack you in the passage to the E room is also marked as a secret. (sector 125) There is no way to enter the cage, and so this secret is unreachable.
The pit that the passage to the E room curves around also counts as a secret. (sector 131) Press the wall at the south of the pit to raise the floor and escape. On skill 4 or higher, you will find two boxes of ammo here. Note that on skill 3 or higher, you may have trouble entering this secret, as one half of each opening into the the pit is blocked by a barrel.
The window immediately south of secret #10 counts as a secret. (sector 175) It cannot be reached, as you can neither climb nor fit through the window.
The room seen behind secret #11 counts as a secret, as well. (sector 174) It is likewise unreachable, as there is no way to enter the room.