SMTP is the "Simple Mail Transport Protocol". Its the protocol being used for transmitting e-mails over the Internet. It was designed for delivering e-mails from a mail user agent (such as Eudora or MS Outlook) to a mail server.
JMS (Java Message Server) is a Java API which was designed for application-to-application messaging.
The only correlation is that both technologies are intended for transmitting "messages". However, the application areas are very different: Person-to-person e-mailing versus application-to-application communication.
This was first published in January 2002