If you are missing a specific piece, the Gemcraft Wiki maintains a full list of click-coordinates for every secret fragment.
Check the corners of the achievement or statistics menus. GemCraft - Chasing Shadows
While the game encourages exploration, these are the common locations associated with the "paper" secrets: If you are missing a specific piece, the
Look for a blank space on the world map that doesn't fit the grid (usually in the bottom right area). GemCraft - Chasing Shadows
Watch for "cracks" in the UI or parchment that looks slightly different from the rest of the background.
Your cursor will often change or a tooltip will flicker when hovering over a secret element.