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1.
Reading, writing, and arithmetic (i.e. mathematics). They're considered the three fundamentals everyone should learn by the time they finish elementary education... well hopefully.

Yes, only one of the Three R's actually starts with the letter 'r'. The phrase originally started as a joke, but today it's more of an idiom.
It's a terrible school; the children are not even taught the three R's.
by Willow weep for me February 13, 2008
 
2.
The name for underground assassinations, anyone in its path will undergo the three Rs.

The roof, the river or the revolver.
John: I lost the bag
Pete: That bag had a half a million in it, if you don't find that bag it's the three Rs for us; The roof, the river or the revolver!
by GraingerIV April 07, 2009