Java Mail – API siting on top of  e-mail protocols like SMTP, POP, IMAP – essentially same stuff e-mail clients like MS outlook use  .. hence make sense if at least on one side of conversation we have human.

JMS Queue – is asynchronous point-to-point communication between systems

JavaMail API provides a platform independent and protocol independent framework to build Java technology based email client applications. The JavaMail API provides facilities for reading and sending email. The JavaMail API is implemented as a Java optional package that can be used on JDK/JRE 1.4 or higher with any operating system. The JavaMail API is also a required part of the Java Platform, Enterprise Edition (Java EE). JavaMail is completely written in Java and will run on any operating system that supports the required version of the JDK.

Java Message Services, JMS, is Sun's standard API for message queuing systems. Message queuing systems form the front-line interface between businesses (B2B) and for Enterprise Application Integration (EAI). As such, message queuing systems are often called "middleware" because they operate in the middle -- between other systems and between enterprises. JMS offers a number of advantages over older Message queuing systems. First, JMS has two message protocols: point to point and pub/sub instead of only one, as many earlier middleware systems did. Additionally, JMS also doesn't care whether you use a wire or wireless protocol, and provide different levels of message delivery assurance as well.