When you get to the second area with bouncers, when you're on the final ledge, turn left, you'll notice a small ledge. Jump on it to be catapulted above the ledge you were previously standing on and collect some ammo. This will spawn a Sirian Werebull below in the final ledge though.
As soon as you get out of the temple, turn around and look up. You'll see an Invulnerability powerup on a ledge. Shoot a rocket to the ledge to bring down the powerup. (Note that this secret will only be registered in the Serious Sam HD version of this level. A bug prevents it from being registered in the original version).
In the right temple, with the male jaguar, when Sam says he smells some "serious firepower", slide on the right side, in the below ledge. You'll see a differently colored part on the wall, shoot a rocket at it to reveal a minigun. This secret does not exist in the Palenque Demo.
In the upper right corner of the valley, with a giant boulder on top of a mountain, there's an Extra Large Armor. Collect it, and watch out for the rock, as it will fall once you pick it up, and some Werebulls will spawn.
Diagonally opposite of #4, in the lower left corner of the valley, with the Crollywood sign on the mountain, walk towards its end to register the "Crollywood Movie Studio" secret.
(HD only) In the left temple, with the female jaguar, before entering the cave, jump down below the bridge, then jump on the beams that support the bridge until you reach a Super Armor.
(Fusion HD only) Before the hall with the spikes, in the left temple with the female jaguar, blast all the six jaguar heads surrounding you to enable a "secret" teleport that will take you to the other side of the hall, without having to pass the spikes. This doesn't count as a secret in all previous versions of the game.
Still in the left temple, with the female jaguar, after passing through the hall with the spikes, there's a bouncer somewhere in the room, in the upper right corner, next to a health vial. Use it to be catapulted in the above beam of the room and collect some sniper ammo and an Extra Large Armor (only by picking up the armor the secret will register).
In the "middle" pyramid, with the crystal skull, enter the hut on the left to find a hidden stash of bullets.
Still in the "middle" pyramid, with the crystal skull, go behind the hut on the right to find a secret Medium Health.
In the classic version of this level, the Invulnerability secret does not register. This is because the trigger for the secret is expecting the player to pick up a Serious Damage after destroying the ledge. However, since there is no Serious Damage on the ledge, the secret will never register. This is most likely because the default "powerup" entity in Serious Editor 1 is the Invulnerability, and Croteam never got around to changing it into a Serious Damage. This has been fixed in the Serious Sam HD version of this level.