Cletus did a great job at summarizing this comparison. Hibernate works well when you control the data model and is more object-centric while iBATIS works well when you need to integrate with an existing database and is more data-centric.
Also I think that Hibernate has a bit more of learning curve. With iBATIS, it's pretty easy to know what is going on while more "magic" happens with Hibernate. In other words, newbies might find iBatis easier to use and to understand.
But I'm not saying that you should prefer iBatis, iBatis and Hibernate are just different as said above.
And by the way, if you go for Hibernate, maybe consider using standardized JPA and EJB 3.0 (JSR-220) object/relational mapping annotations provided by Hibernate Annotations.
