My first guess would be that it is related to the transmission as it goes away after you put the car in Neutral. However there are other factors at play. The engine being under load at a specific RPM. As was suggested timing, injectors, and poorly adjusted valves (compression?) could also combine for some strange harmonics.
I'd start with the motor. You can test the above without throwing unnecessary parts at the car and they are all just prudent preventative maintenance. With the motor ruled out you can start to look at the transmission or other possibilities.