Spring was developed as an alternative to EJB right from its inception, so the answer is of course you can use Spring in place of EJBs.
If there's an "advantage" to using EJBs, I'd say that it would depend on the skills of your team. If you have no Spring expertise, and lots of EJB experience, then maybe sticking with EJB 3.0 is a good move.
App servers written to support the EJB standard can, in theory, be ported from one compliant Java EE app server to another. But that means staying away from any and all vendor-specific extensions that lock you in to one vendor.
Spring ports easily between app servers (e.g., WebLogic, Tomcat, JBOSS, etc.) because it doesn't depend on them.
However, you are locked into Spring.
Spring encourages good OO design practices (e.g., interfaces, layers, separation of concerns) that benefit any problem they touch, even if you decide to switch to Guice or another DI framework.
Update: This question and answer are five years old in 2014. It needs to be said that the world of programming and application development have changed a great deal in that time.
It's no longer just a choice between Java or C#, Spring or EJBs. With vert.x it's possible to eschew Java EE altogether. You can write highly scalable, polyglot applications without an app server.
Update: It's Mar 2016 now. Spring Boot offers an even better way to write applications without Java EE app servers. You can create an executable JAR and run it on a JVM.
I wonder if Oracle will continue to support the Java EE spec. Web services have taken over for EJBs. The EJB solution is dead. (Just my opinion.)