i agree with kain, get a Japana Rail Pass - theyre expensive, but if you plan to travel alot theyre so worth it - you can get teh bullet train for free (normally about £300), the ring line in tokyo and nearly all teh local railway systems in kyoto and osaka - was VERY useful for me
metro travel in central tokyo is really simple and cheap too - its all a standard fayre system about 80pence to travel accross tokyo - excellent
there are buses but theyre apparently kinda unreliable and the taxis are extortionate!