Majora's Mask Stray Fairies
We have all the Stray Fairies for the Nintendo 3DS and the Nintendo 64 versions below. There are some slight differences but each version has screenshots and descriptions for all of the stray fairies found in the game.
Nintendo 3DS Version
Stray Fairy #7 - In the dark room with a bunch of Black Boes and a few unlit torches. Defeat all the Boes to get the fairy.
Stray Fairy #12 - In the room with the multiple Eenos, use the Lens of Truth to find the fairy.
Great Bay Temple
Stray Fairy #7 - In the narrow hallway room after getting the Dungeon Map, there are a number of Bio Deku Babas. Defeat them all to get the fairy.
Stray Fairy #9 - Then use the Hookshot on the target above to reach the higher level of this room where the stray fairy can be found.
Stone Tower Temple
Stray Fairy #10 - In the large, multiple-floor room, play the Elegy of Emptiness on a floor switch to create a treasure chest.
Stray Fairy #11 - Defeat Wizzrobe.
Stray Fairy #12 - Back in the entrance room, step on the floor switch next to the Death Armos. The fairy is then acquired when the temple is returned to normal.
Stray Fairy #15 - In the room just before the Temple boss while the dungeon is inverted, hit the crystal switch. Revert the dungeon and return to Hiploop room to get the fairy.
Nintendo 64 Version
9. If you moved the "double blocks" in an earlier room into a little slot, there is another Stray Fairy you can get now. Push the block LEFT, UP, LEFT. Jump onto the second platform and enter the door. In this familiar room, if you placed the double blocks in the right place (where it fell into a slot), you can use them to jump to the other side. Open the chest when you get there to claim your prize.
15. In the main room, there is a small hidden cubby that holds a chest containing the last Stray Fairy. You can see where it is by the patch of ice hanging off the ledge (or use your Lens of Truth). To get to it, you'll have to jump from a higher level, by using the Goron Mask, Bunny Hood or Deku Mask to roll, jump, spin or fly (using the flower on the top floor) towards it. If you're lucky, you'll land in there. The best way in my opinion is to stand on top of the pillar in the center of the room after you've punched out the ice cylinders, and spin towards the cubby with the Deku Mask. You will just make it, no problem. Once you get it, you can salvage some ascending by using the flower there to fly to the third floor on your left.
Great Bay Temple
9. Get to the YELLOW platform and face the wall opposite the door. If you look up, you'll notice some metal grating separating you from a small area up there. In front (above) of you is a hole in the grating with a target nearby on the ceiling. Use your Ice Arrows to create platforms and get near the far wall, then turn around and Hookshot the target. It may take a couple of tries, but once you get up there, in the center you'll find a chest.
11. When you've frozen the waterwheel in this room, walk part way across the paddles, then turn right. When you get to the six blades (only two are accessible, pointing in either diagonal direction) climb onto the one on your right. Climb to the end of it. You'll notice that straight ahead is a small hole in the wall with a chest. Hookshot the chest and open it.
Stone Tower Temple
3.2. There's a small platform at the top of the room with a flame on it. If you stepped on a switch in this room (that was filled with water before) earlier, there's a chest here now. Go to the small platform on the right side of the room with a switch on it. Play the Elegy of Emptiness to keep it down, then fly up and claim your prize.
6. There is a chest on the other side that is surrounded by fire. Down below, there is a switch you can stop on as a Goron to put the fire out, but it's on fire as well. Use a Goron Stomp (A + B) on the Goron Switch on the first side, then run and roll to the other side and step on the switch before the fire returns. This will put out both flames. When you get to the other side later, open the chest.
14. Go back to the room with the water, the bridge and the hand enemy. Use it to throw you up onto the ledge. Use a Bomb or a Spin Attack to hit the crystal switch to make a chest appear in the other area. Go to the other side by either going back through the various rooms, using a dolphin jump with the Zora Mask to get back on the ledge, or play the Song of Soaring to get back to the start of the temple and go through the two doors on your left. The last way gets my vote for the best. Use a Light Arrow to remove the Sun Block. Kill the Beamos using a Bomb and open the chest.