As we switch over to ejb3 annotations, we are trying to use all of our .hbm.xml files to output the new pojo's with annotations, the problem is that when we run hbm2java in our hibernate tool task, it does not create the where annotation for some manytomany relationships. As well, we would like the pojo's to contain @NamedQueries annotaitons as well, is there a way to make hbm2java do this.

I can only imagine what else it is missing in the process.

yes - improve the templates to be more complete.

you can submit patches and/or report issues with testcases showing the missing "conversion" ..both will help.