Since OSGi modifies the class loading, most of the tools available don't work in an OSGi environment.
Marc R. Hoffmann describes a basic approach for solving this problem on the eclemma research site.
All jar files needed to run the eclemma/emma code coverage tool with OSGiUnit tests are now part of the osgiunit.externals project.
There is a second build file (build_cc.xml (osgiunit.svn.sourceforge.net)) in the osgiunit.examples project which shows how to run the eclemma and emma tools to create a coverage report.
Simply run
ant -f build_cc.xml clean JUnit emma-report
and find the HTML report in the file coverage/coverage.html (osgiunit.sourceforge.net).
One problem currently exists: The coverage report shows only the functions and the number of blocks covered, but does not show the sourcecode lines.
Coverage report from the osgiunit.example project (osgiunit.sourceforge.net)