Dark Passage (map name: ty2)

Swim to your left. Ignore the door -- it leads back to near the start. Instead, push the crate under the broken stairs/ladder and climb up (jump and run).

Don't forget the goods on the crate in the next room. Activate the switch in the room above the broken stairs. This opens the barrier by the train tunnel next to the waterfall. Go there, walk to the end, open a few huge doors by activating the switches on the wall, and move along to the next level.

Trainyards (map name: ty3)

Jump across the open area on the flatbed trailer where the block was and to the walkway/ledge on the other side. Go through the door on the left, then another door, and walk out into the train yard. The train car in the second row, on the left (with the two thugs guarding the door) opens, and has a nice cache of goods inside. The other cars do not open, but the one on the far right has a ladder on the back of it.

Climb the ladder on the back of the far right train car, then jump your way back, from car to car, to the concrete walkway above the door you entered the yard from. The jumps look far, but are pretty easy if you make sure you don't jump too soon. The door on the right leads back where you came from (was locked on the other side), so go left and jump/climb down into the crate room. Move the crate on the left into the far right corner and climb up the crate tower for some grenades.

Exit the crate room using the door on the far left (relative to your entrance). Activate the switch there, and walk through the big door that opens when you do. At the next set of train cars you'll need to pull the old "release the cars trick" again. Look for a wheel shaped switch between the cars and activate it. One car will roll away, revealing a ladder on the car. Climb the ladder on the train car you just let roll, jump off to the left-hand ledge (behind you after climbing, really). Activate the switch on the wall there, then climb back on the train and jump off the other side, to the other ledge. Open the second overhead door (the one not blocked partially by crates) and keep walking until you find the room with the two hooks on ropes hanging from the grated ceiling. Kill the enemies, then walk up to the control panel and activate the switch on the left twice.

The first time moves the nearest hook all the way to the left, the second time stops it in the middle. Climb up the hook, get the fuse (item fuse) and the health if you need it, then head back down. Go back outside, enter the other door, insert the fuse into the panel (just walk up to it after you've found the fuse).

Then climb the ladder that lowers and walk across the catwalk. Walk down the stairs (don't miss the clip hidden under the stairwell if you need ammo), walk outside amid still more trains, and keep right, walking down the tunnel where you'll find another switch to open a huge door which leads to the next level.