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java.exe is for running the class file. As per my understanding, it’s not used for compiling Java code. Then what is the use of java.exe at this location on my system: C:\Program Files\Java\jdk1.6.0\bin\java.exe
Like you said, it’s to run the compiled Java code. And it’s there so that you can use easily include it in a CLASS-PATH variable(in Windows it’ll help you run java from command line ).
The JDK subsumes the JRE – i.e if you get the JDK you’lll also get all the JRE stuff. But if you download only JRE, you won’t have everything