使用DB开发Java的最佳方法

I've experience with Toplink to translate objects to database and vica versa. But this was all part of a JSP site and now I did some EJB stuff with it to. Now is my question: is it good to work with stuff like Toplink in a Java Desktop application or is it more common to use native sql stuff from Java?I've experience with Toplink to translate objec