I took an overnight bus from Tokyo to Kyoto. I booked it through http://willerexpress.com/ and got discount price for 5100 yen. I think it’s a quite a good deal. I chose to get off in front of Hotel Centnovum Kyoto because when I checked on the map, it looked close to a train station. And I made a right decision, turned out it’s Kyoto Station. Haha.