Secret Monkeys are monkeys that you can't get (in most situations) until you beat the game for the first time and come back with a different Gadget or Morph (Persona) that isn't obtainable until beating the game prior. The Secret Monkeys are hidden and require you to use the gadget/morph to find them.
Secret Monkeys in Ape Escape 2 Edit
In Ape Escape 2 to catch Secret Monkeys you must first finish the game (beat the Moon Base level once) to unlock the Magic Punch gadget. Once you obtain the Magic Punch it is then possible to break open certain objects to find Secret Monkeys. There is usually one Secret Monkey per level. However three of the secret monkeys don't require the Magic Punch gadget and just appear after beating the Moon Base level.
Secret Monkeys in Ape Escape 3 Edit
In Ape Escape 3 to find and catch Secret Monkeys you must first finish the game to unlock the Super Monkey Morph. When you transform into the Super Monkey Morph you will be able to sniff out hidden rooms filled with Secret Monkeys by following the yellow wavy lines.