It's hard to squeeze a lot in....I know b/c I had an 18 hour layover in Rome and I went crazy running around trying to see it all. I would recommend getting on a double decker bus tour; you can hop on and off all over the city.
Colosseum, Vatican City (Sistine Chapel, St. Peter's square, Swiss guards), Trevi Fountain and the Spanish Steps, the Panthenon, the Forum...
There is so much to see but those are the highlights in my opinion and you can't do much more in a short amount of time.
Flight to Tokyo: 92,000 yen
Metro to Ginza shopping district: 160 yen
Watching middle-aged Japanese woman dance to U2: priceless