No real secret areas, but if you go to the very left as soon as heading out of the starting area, and run along the boxes you should find an open one with a shieldbelt.
Go underwater, and make sure you have a light source, and while under water look in the direction of the arrow.
Leads to picture below. Go through that passage way and down the flight of stairs on your right.
In the room with the second wave of krall. Jump to the shaded area after going up lift.
Go in the water (leads to picture below)
In the area that is open after defeating titan and first wave of krall and contains switch to the area with second wave of krall. Fire at the circled area.(The very front considering you are facing the same way as the picture above)
This is a tricky one. You need to push a barrel (should be found by the staircase in this room) and get it under the torch holder. Then jump on the barrel and jump and touch the bottom of the torch holder.
After defeating the brutes in the courtyard (open area with grass) go up the ramps and follow the nali, as he opens a door.
The nali in the right hall of the cells will run to a useless area getting ambushed by a skaarj
The nali in the left hall of the cells will run to the barn (refer to last nalicastle secret) showing a cool cutscene!
Press the book sticking out of the bookshelf (I shot it with my Dispersion Pistol so you can see its general area.)
This is the staircase leading to the balcony part of the secret area above. (use this reward with your ASMD and the boss should be no problem :))
This is just outside of the small area with the giant bell. Just run along the red line to get to this cool area (alternatively the nali in one of the cells will take you here revealing a very cool scene)
Hop on down!
Follow this path, go up the ramp and stop in the middle of the bridge (leads to picture below)
You must be quick with this one, the very second you get the superhealth jump on the large pipe, otherwise you'll end up dead.
There's also a very strange area. At the beggining when you are done going up, if you look behind you, there should be a door. Use the 'ghost' command to get through it and you'll be in a room with a lot of weapons!