1. Read your config file, connect to the remote JNDI context of each server at runtime and invoke your EJB manually. 2. Dynamically generate an XML DD with the fully resolved JNDI name/remote EJB name for each of your servers. Loop through these EJB references at runtime and invoke them. 3. Re-write the EJBs instances on each server as MDBs. Have these MDBs listen to single, centralized JMS topic. You can then trigger all the MDBs by sending a single "activate" message to this single JMS topic.
If you can use JMS, I recommend option 3, it is the most robust and loosely coupled design. If you cannot, I would go for option 1. It is simpler and more flexible.
Independent Consultant — Author, EJB 3 in Action — Expert Group Member, Java EE 6 and EJB 3.1