Over these years I came across many API’s and used it in my project. Finally I decided to put it out and see what other folks are using. Here is my comprehensive list

iBATIS (http://ibatis.apache.org/ )- O/R mapping API where the approach is bottom to top (mapping for existing database)
I found this better than Hibernate(3.x prior) where it doesn't support stored procedures.Check it out.
JIBX http://jibx.sourceforge.net/ framework for binding XML data to Java objects.I came across this API from Java user group meeting