These are the minigames that you can (and are required to) do during the game.
Fishing
This is the first minigame you will come across while on El Dorado's ship. To fish, go to the end of a pier and press 
. Your dog will throw the line into the water, and at any point after that the word 'FISH' will appear. You need to pull the Wii remote up like you are pulling in a real fish. You need to repeat this until you have caught the fish, but if you pull too hard or soft, the fish will escape.
Bug Catching
You will learn how to catch bugs when Clark, one of the Victory Gang dogs, will challenge you to catch a butterfly. To catch a bug, look around the level until you see something tiny hopping around or flying or crawling, and press to have a go at catching it. A meter will appear at the bottom of the screen and there will be an orange bar moving back and forth when the bug is moving. You need to press again when the little blue line is over the orange bar, and you will catch it. If you miss, the bug will get away but it will still be flying around nearby.