CLR
CLR is nothing but Common Language Runtime.the code which is in the environment of CLR is called managed code. Every language has runtime, but in case of .Net there is CLR.so that, it has some responsibilities that is to take care of the execution of code...,
Other responsibilites :
Garbage collection, in that it will remove the object which are not refered for long time.using I disposable interface with dispose() method.

CLS
Common Language Spefication
This is a Guideline that to communicate smoothly with other .Net Languages. CLS is set of language rules that defines the language standards for dotnet.

CTS
Common Type System
This is used to communicate with other language. That means to match the data types, library methods, classes..., CTS make us feel it as a common environment without considering the language.
Example in vb we have int and in c++ we have long so that in one case they are not compatiable with each other so
that CTS palys important role with using System.int32