The Beach

These mossy rocks look like a Kingler when viewed from the right angle.

The Tunnel

If you get Zapdos to turn on the power, this makes the wall look like a Pinsir.

The Volcano

Toss a Pester Ball inside the crater around the Rapidash to make this Koffing cloud appear.

The River

After you play the Poké Flute to the Vileplume take a picture of these rocks that look like a Cubone.

The Cave

Across from the Weepinbell's pond, take a picture of the sparkling dots. They turn out to look like Mewtwo.

The Valley

The Mountains at the start of the stage seem to resemble a Dugtrio.