Kura Puzzles are unlocked the same way Wallpapers are, which is when certain events are triggered. Here is a list of all 56 puzzles you can currently unlock.
#2 - Painter-kun's Painting - Interact with Painter-kun in the Art Gallery.
#3 - Sign - When you first enter Sign World.
#4 - Green Juice - Interact with Aojiru ("Cripple-Tan") at the Hospital.
#5 - Three ┏(∵)┛ - When you first enter the Bowling Zone.
#7 - もっきゅっ! - Interact with the blob NPCs in the Marijuana Goddess World.
#8 - Grinning Eyes - After you go up the ladder to Tapir-San's Place.
#9 - Blue People - Unlock Wallpaper #97.
#12 - Hakoko & Megusuri Uri - Interact with Hakoko at the Eyeball Shop.
#13 - Darkness - When you go through the tunnel on the Highway.
#14 - Pipe Organ - Interact with the Blue Beret Twin in the Dark Room.
#16 - Octopus - When you use the Fairy effect on Tako Otoko in Atlantis.
#18 - Odoriko-san - Interact with Odorika in Red Streetlight World (you don't need the Maiko effect).
#19 - Gakuran - Interact with Gakuran-kun.
#20 - Stardust - When you enter Space from Tapir-San's Place.
#21 - Rune Mark - When you first enter Theatre World.
#22 - Primitive Present - When you first enter the Tribe Settlement.
#24 - The Grudge - Cutting the rope at the well in Fairy Tale Woods and getting captured.
#25 - Hanging Child - When you encounter Koshukei-tan in Graffiti Maze.
#26 - Are You Going Again? - Interact with Megusuri Uri outside his shop in Visine World.
#27 - The Playing Is... - Interact with the clown that plays the accordion at the Underwater Amusement Park.
#28 - Mask - When you chainsaw Painter-kun in the Art Gallery.
#30 - Black Witch - After chainsawing the sane Shadow Woman in Forest World, going underground and then emerging.
#31 - Eyeball Human - When you encounter the Eyeball People in the Spelling Room.
#33 - Smile - When you first enter Guts World.
#34 - End - When you pass by the meteor along Highway (near the tunnel).
#37 - Candy Girl - When you use the Cake effect on Sweets Musume in Cutlery World.
#38 - Tear - When you chainsaw a stick person in the Penguin Game.
#39 - May I Eat? - When you use the Cake effect on Sweets Musume in Cutlery World.
#40 - My Name - When you spell "Urotsuki" in the Spelling Room.
#41 - Bug - When entering Seishonen's room and it is glitched.
#42 - RPG-7_Untitled - When you get the chasers to surround you in Urotsuki's Dream Apartments, then leave the room and get attacked
#43 - Uro & T-Shirt-kun - Interact with the blue NPC at the end of the Arrow Maze.
#44 - Room Window - When you go through the black window in the Never-Ending Hallway.
#45 - Each World - When you go through all of the Nexus portals.
#46 - 'NULL MI - After looking up at the ceiling of the inescapable room in Binary World's tower.
#47 - Idenshideau - After meeting the fish in the jar in Green Binary World.
#48 - ぜんまいの鶏 - When you kill the angel priest in Fountain World
#49 - ジェイア - When you are chainsawed by the hockey mask girl in GALAXY Town
#50 - 暗彩光を飛ぶ - After encountering It Came from Behind in the Neon City.
#51 - こーひーうろつき - When you have a cup of coffee at the cafe in the Eyeball Archives.
#52 - 退水の先に - When you approach the pink structure in the Polluted Swamp
#53 - 退水の先に - When you find the caged Shadow Bird in the Halloween Forest part of the Cat Cemetery.
#55 - 揺蕩うくじら - When you enter Paradise for the first time.
#56 - When you enter the room with smiling blobs in the Overgrown Condominium.