Are there any free tools for Java (preferably Eclipse) that can give metrics on both how frequently code is executed (based on a recorded run) and do a side by side with coverage? I'm not sure if there is already a metric for measuring this but it seems it would be an interesting one to see.
Are you looking for a Java profiler (something that gives you function call counts and elapsed execution times)? If so, you might want to look at the Eclipse Test & Performance Tools Platform. It doesn't look like it will give you a side-by-side comparison of two pieces of code, but it might be worth looking at.
do you mean running the application as in production ? if in dev environ ...not sure if this is what you are looking for - http://insectj.sourceforge.net/
The SD Java Profiler collects profiling data in a way that generalizes test coverage. So if you have its profile data displayed, you have the test coverage data effectively displayed too; there's no need for a side-by-side comparison.
Not free, and doesn't plug into eclipse yet, but does use a Java GUI.