What is the content of the $CLASSPATH variable in El Capitan?
First, I found out that my Yosemite Installation has also no CLASSPATH set.
Second, when issueing

$ java -help


it directed me to the URL:

Java SE documentation

Klicking there led me to How Java Runtime finds classes and within there it is written:


  "[…] User classes are classes that are defined by developers and third parties and that do not take advantage of the extension mechanism. You identify the location of these classes with the -classpath option on the command line (preferred) or with the CLASSPATH environment variable. See Setting the Class Path.[…]"


Effectively it says "put your classes wherever you want and just run java -classpath &lt;userclassdirectory&gt;. 

Just take time to read the complete document.