from kobe it only takes about 1 hour by train to kyoto, and costs 1100yen, very economical :) also the kyoto train/bus station is a very cool architectural complex! just try to run up the stairs and you'll see a great view of the city!!! to go to tokyo cheaply, you can catch the night bus in osaka, you can get there under ichiman!!! pic...last night, waiting for the bus in osaka station.
KYOTO STATION: If you arrive by the JR (JAPAN RAIL) this is your first contact with Kyoto. Kyoto City TIC is located on the 2nd floor main concourse (Tel: 075-343 6655). Also, check out the station's shopping area called THE CUBE which has shops specialising in local food products & Kyoto crafts.
Besides being the main train hub, Kyoto station is a sight all of itself. its built as a large open V.
Kyoto Train Station is new and modern and looks awsome. It has a megga shopping area compiled around it is a really cool place.
Kyoto Station is the main station from Kyoto and the place where you arrive and leave by JR. The station itself is also worth a visit. The architectur is quite nice.
Kyoto is a great place to base yourself to explore Japan. If you have a JR pass you have access to the majority of the sights in the country no more than 3 hours away by Shinkansen (Bullet Train).
A quick glance at this map of the Kyoto JR Station and you'll think for a moment you must be on board the starship Enterprise.