Climb the Mushroom Stairway in the center of the hub world. When you reach Treetrunk Peak at the top of the tree, you'll see this.
Tibbet will give you this after completing Iron Jaw Gulch.
After completing Motleyville, you'll have access to The Under-Hollow. Head inside to find this by a fountain.
After Flynn's crash, turn around to see this just behind the level start.
After defeating the Greeble Screwball, go left around the rock face to find this.
Continue down the path until you reach the Water/Fire Dual Element Gate. Use a Swap Force character that matches this (or, if you're playing co-op, one of each type) to open the way.
After learning how to push blocks in Old Treetop Terrace, hang right before crossing the bridge to find another goodie.
Just beyond said bridge is a series of ledges to the right. Hop up them to collect your first Story Scroll.
After taking out your first Chompy Pod, look to your left for some descending ledges. Head down to enter a hidden area, Honey Trove. After pushing the block to cross the bridge, push it back across, then north. Once it falls into place, you can jump onto it to reach the ledge where the collectible sits.
Return to the main area above Honey Trove and bear left after the bridge. Use and Air Skylander to open the Elemntal Gate here. Complete the shooting minigame at the end of the area to receive this is a reward.
A little later, you'll have to push more blocks in Long Worn Hollow. After dropping the lower one off of the rock bridge, head to where it fell. You'll be able to reach the last piece of Flynn's Missing Stuff by jumping on it.