I log whatever is entered in the companies crew scheduling system as this is the only legal way that i can validate my flight time for any future employers. The system logs block out to block in for purposes of flight, therefore (theoretically) we would log the 3 hour wait in JFK, but we wouldn't log repositioning times after dropping off passengers (but we are paid for this time).
By the same logic, we can log "sleeping time" during augmented or double crew flights.
Mutt