Crystal 1: In the Knight Academy, in Link’s room, on the table.
Crystal 2: Near the Knight Academy’s top floor doors.
Crystal 3: In the Sparring Hall. Send the Beetle into the rafter’s above the instructor’s stand.
Crystal 4: South and downstairs of the Knight Academy. At the bottom, go left and cross the wooden bridge.
Crystal 5: Can be found in the west portion of Skyloft. Near the southwestern windmill and climb down the vinery to the ledge below.
Crystal 6: Inside Orielle and Parrow’s house in Skyloft.
Crystal 7: Behind the tree in the eastern pumpkin field of Skyloft.
Crystal 8: On the lower portion of the Skyloft Light Tower.
Crystal 9: Near the Skyloft Waterfall Cave. Go through it and check around the heart flower plants.
Crystal 10: In Skyloft, where your Loftwing was imprisoned past the Waterfall Cave.
Crystal 11: Atop the Skyloft waterfall. You’ll need to use the Clawshots to get there, then the Hook Beetle to grab the Gratitude Crystal near the edge.
Crystal 12: In Zelda’s room of the Knight Academy. Using your Clawshots from the Academy roof, get into the chimney, then crawl through the tunnel to find the Crystal. (Also check the dresser for a Piece of Heart.)
Crystal 13: Outside the main Pumpkin Landing building, behind the pots in the shed.
Crystal 14: Inside the main Pumpkin Landing building, on the first dresser of the second floor.
Crystal 15: On Beedle’s Island. Sleep in Beedle’s Airshop during the day on Skyloft, then exit the ship at night. Look above the propellers on the shop roof; use the Hook Beetle to get the Gratitude Crystal.