You should definitely give a try to JaCoCo. Its integration with Sonar allows to benefit from new features, for example :
merge coverage by unit and integration tests. See http://www.sonarsource.org/sonar-3-3-in-screenshots/
track the relations between tests and tested code (since sonar 3.5). You can find a screenshot on the documentation page: http://docs.codehaus.org/display/SONAR/Resource+Viewer#ResourceViewer-CoverageTab