The Middle East
*-not including palestinian territories in the west bank and the Gaza strip.
The train system in Israel is under one national company, so all train times, destinations and prices can be viewed on the Israel Railways site.
Train tickets are bought at the station, either from a cashier or an automatic machine.
There are several bus companies in Israel, most of them operate in different areas. This site allows to search for busses from all companies, and has links to all the sites of the different companies. The site gives both lines inside cities and between cities. The busses include busses to territories under Israeli control in the west bank.
Tickets are usually bought from the driver in the bus. If you get to the bus in a central station, a ticket can be bought in the station, but isn't mandatory.
The only exception is buses to Eilat. tickets to Eilat and its surrounding need to be bought in advance on-line or at a central bus station. Site for Eilat booking
Inside Jerusalem exists a light rail, their site
An underground train exists only in Haifa, and it has only 6 stations, the Carmelit's site
Flights are available to/from Haifa, Tel-Aviv and Eilat. Tickets are bought trough the airline site, or through travel agencies or flight booking sites. Sites for the airliners: El-Al, Arkia and Israir (no English site for Israir).