Didn't Mojang add cocabeans to the update in jungle tree Diamond hoes Are super easy just craft one mob spawners just xray or have a pretty decent headsetSaddles - Only found in chests in dungeons.
Record - Supposedly only gained by tricking skeleton into shooting a creeper with its arrow. However, I've obtained one by killing a creeper with my own bow/arrow before. Also found in dungeon chests.
Cocoa Beans - Found in abandoned mineshaft chests and rarely from Jungle trees
Cookies by proxy, as they are made from cocoa beans
Ender Pearls - A rare drop from a rare mob.
Blaze Rods - Flying mobs in the nether; hazardous to kill. Can be used to make a few other ingredients via Blaze Powder
Ghast Tear - Prone to falling into lava when you kill the Ghast
Mossy Cobblestone - Only/always found in dungeons
Netherbrick - only obtainable from Nether fortresses.
Bedrock/Adminium - Cannot be mined, found at bottom of map. Must be spawned through console to place.
Sponge, Gear - Cannot be found or made. Must be spawned through console.
Ice - currently unobtainable as a block, can only be made in a snow biome.
End portal and End portal frame - 27 end portal blocks per world and 36 end portal frame blocks. Possibly less because of terrain generation.
Record (omg, getting them in SP is sooo annoying)
(Strongholds not necessarily items but they're pretty rare.. oh and I have 3 of those )
And not necessarily in that order
Three strongholds spawn per world
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This depends way too much on your play style (Miners will have more diamond, Adventurers more circle bricks, mechanics will have used up more red stone etc...)
It also depends on the version you started in (Ice, no ice, ice again, cocoa beans, etc..)
And then there is farms.. Without my blaze farm I am pretty much sure blaze rods would be rare in my world.
All I know is the blocks I am holding on to. Like the old wooden slabs. Every day they are becoming rarer by time, gnagna...