Then it depends on what you want to do with your SCBCD. If you're about to work on a project using EJB2.X, then SCBCD 1.3. If you're curious about how crappy EJB2.X were, then go for SCBCD 1.3. I've passed 1.3 mainly because I wanted to know more about old beans, before dealing with new stuff.
If you don't care about those rotten 2.X beans, and just want to learn about lastest stuff, then SCBCD 5.0 is for you. You'll learn about how cool EJB3.0 are. But be careful. Information about SCBCD 5.0 is scarce. There are a few good books about EJB3.0, but nothing aimed at the exam. So you'll probably have to use the specs too.
I hope you'll make up your mind. And don't forget to visit the SCBCD Links.
I completely agree with Satou. I'm currently preparing for SCBCD 1.3 because my company is still using it. Frankly speaking, I hate EJB 2.x, especially the CMP entity bean. It's whole of mess. I'll go for SCBCD 5.0 after I clear SCBCD 1.3.
BTW, if your aim is solely to get the cert, SCBCD 1.3 is a way to go. HFEJB is a very good book for SCBCD 1.3. Currently, there aren't any books for SCBCD 5.0 yet.
SCJP 5.0, SCWCD 1.4, SCBCD 1.3, SCDJWS 1.4