The rarest in terms of availability are the Ender Egg, although this is easy to obtain, there is only 1 in the entire Minecraft world.
Next is endstone, there are thousands of of and it's not hard to obtain.
Mossy cobble is rare, but there is no loss of it in the world. There is a little under a stack per dungeon, and there are a few stacks in a temple.
Saddles are particularly rare, although I have seven of them in my SP world.
The most difficult ore to find are Emeralds, although you can get hundreds of those from sneaky villager trading.
Diamonds are the most useful but are "infinite", although rare chunkwise.
Cracked and Mossy Stone Bricks are finite, only found in strongholds which 3 are in existence in the entire world.
Blaze rods are not rare under the right circumstances, blazes have spawners which make the actually easy to farm if you enclose them.
Netherwart can only be found in Nether Fortresses, like Blazes.
Ghast tears are not difficult to get, except that there is a high likelyhood they fall in lava. Magma cream can be crafted from a slime ball and blaze powder. Not that rare.
Dirt and stone durr! Joking, I say (most rarest to least rarest):
1: End Portal
2: Dragon Egg
5: Music Disks (pretty hard to get for me as the creeper blows the skeleton up if the skeleton hits it)
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 )
Nothing is rare comparatively, in every world there is the same amount of diamonds, iron, gold, redstone, dirt, sand, etc, as in every world, but there are less diamonds than anything else, so diamond blocks would be the rarest.
There are different amounts of diamonds and all the blocks in all worlds.
Renewable items are considered the least rarest. I would say the rarest would be a diamond ORE block.