I use a combination of Cobertura, Checkstyle, (Ecl)Emma and Findbugs.
EclEmma is an awesome Eclipse plugin that shows the code coverage by coloring the java source in the editor (screenshot) - the coverage is generated by running a JUnit test. This is really useful when you are trying to figure out which lines are covered in a particular class, or if you want to see just which lines are covered by a single test. This is much more user friendly and useful than generating a report and then looking through the report to see which classes have low coverage.
The Checkstyle and Findbugs Eclipse plugins are also useful, they generate warnings in the editor as you type.
Maven2 has report plugins that work with the above tools to generate reports at build time. We use this to get overall project reports, which are more useful when you want aggregate numbers. These are generated by our CI builds, which run using Continuum.
