Everyone should have Patterns of Enterprise Application Architecture in his bookshelf. This book is not about frameworks as stated in its title (it is about architecture patterns) but, still, it's a, no the bible that everyone should read at least once.
Now, regarding the mentioned technologies or frameworks, I'd suggest:
- EJB 3 in Action by Reza Rahman. Reza is very active on TSS, he is also a member of the Java EE 6 and EJB 3.1 expert groups. This guy just knows what he's talking about. Globally a very good book (covers the Spring integration too).
- If you want a book about Hibernate 3.x, get Java Persistence with Hibernate, which can be considered as the second edition of Hibernate in Action (excellent book).
- If you are still looking for Spring 2.5 literature, Pro Spring 2.5 or Spring Recipe (have a look at this comparison). But I'd consider Pro Spring 3 because this is where to look at now (I haven't read this one though).
Honestly, with the rollout of Java EE 6, Spring 3, I'm not sure you'll find an all-in-one book covering all that very recent stuff (give the authors a few months). If you do, please let me know :)