We've used it quite successfully in a couple of projects. There isn't anything really special that you need to do, aside from reading the reference manual :-) Just make sure that your project references the Hibernate jar and all its dependencies. You can setup your configuration and mapping files however you like - just beware of the classloading issues if you're trying to use them as class resources.
What we like to do around here is create a separate project that holds all of our external, 3rd party libraries. We put all of the Hibernate-related jars in one folder. That makes it easy to associate source & docs with them. Then, to create a Hibernate-based project, just go into the Build Path and add the jars from that other project. The source attachments will follow, so debugging and code hints work well.
You also have a couple of other options when working with WebSphere applications. First, Hibernate can be built as a JCA resource adapter. I have gotten this to work with WebSphere 5.1, but it wasn't real straightforward. I can send you some notes on this process if you're interested. The other way is to directly register the SessionFactory in JNDI by specifying a name in the cfg.xml or properties file. After you build the SessionFactory the first time, it will register itself and you can look it up by name. If you're using Struts, there is even a Struts PlugIn (
http://hibernate.org/105.html) so that the SessionFactory will "magically" be available in JNDI or the ServletContext after Struts finishes its configuration.