will it go only to the servers that support smtp
That's just naming the server not defining the protocol. The part of JavaMail which is protocol dependent is the Transport implementation. The only implementation provided with JavaMail is SMTP. You could write your own if you wanted to communicate with other non-SMTP mail servers.
i want to send e-mail to all the systems what ever they use
How many are you connecting to? Surely you will know what protocol a particular server uses if you are connecting to it, and be able to create the appropriate Transport for a particular session?