The persistent property means that the container is required to persist the timer state to a database. This is important if you need to guarantee that the timer will fire even if the server is taken offline (intentionally or crash). When the server comes back online, it is required to execute missed timers. Setting a timer as persistent also has the side-effect of ensuring that the timer only executes in one server JVM (but not necessarily the one that created it), whatever that means for your product. For example, in a clustered server environment, this typically means that even if EJB module is running on 3 JVMs, exactly one JVM will execute the timer.
persistent=true was the only option available prior to EJB 3.1. Some timer operations are not critical enough to warrant this level of reliability, so the option was added to allow non-persistent timers. Setting a timer as non-persistent also has the side-effect of ensuring it runs in the JVM in which it was created. This can be useful for updating an in-memory cache or static HTML.