Cheapest way to travel from city to city

Hey everyone! Two of my friends and I are going to be going to Tokyo around the 26th of December. It's going to be my second time going to Tokyo and the first time for my friends. Last time I went, I stayed in Tokyo for the duration of my trip, but now I am wanting to travel around to Osaka as well as Kyoto. Is there a cheap way to travel around from Tokyo to Osaka and Kyoto and then back to Tokyo? I was looking at rail prices using Jorudan Co. Ltd and the prices one way were about 13,000 - 15,000 yen. Is there something cheaper than that or is that the best way to travel?

Highway buses, particularly overnight buses, tend to be the cheapest way to travel from city to city.

Your options for travel between Tokyo and Kyoto/Osaka:
http://www.japan-guide.com/e/e2363.html

if time isn't an issue, the juhachi kippu is the cheapest way to travel. but you can only use local trains.
http://www.japan-guide.com/e/e2362.html