There are a total of 5 secrets (I think) in Area49_2 and one semi-secret. Here are screenshots showing each:

Secret 1: This secret is ontop of the containers at the start.

Secret 2: This is through the vents at the army jeep and army truck.

Now to explain how to open this secret... First spam the book on the bookcase (the one in the top left hand corner) and at the same time get someone else to spam the light switch under the water. Here are screenshots showing the book and light:

Then block the opening door with the chair in the room. Like this:

The next part is a little climb bit, if you fall you die, then after there is this:

Pretty rubbish secret huh...

Secret 3: Secret 3 has been done on video. You can see it here: Secret 3 (Warning do not blast out on speakers). The button is near where my aimer is (middle jeep left hand side jump and press):

Secret 4: Secret 4 is after you destroy the helicopter with the shotgun.

There is a button where my aimer is on this picture:

There is another button on this container, the button is in the center of the container door that is opening (The two buttons open the container door):

Gman says "Time to choose" when you press use on him:

Semi-Secret 4: This secret everyone can see but you need god and noclip to see it properly, here it is:

Secret 5: This is near the end of the map in the elevator shaft. The only way to access it is by noclip (admin command).

That concludes Areat49_2 secrets.