Egyptian Railways are easily the most comfortable way to travel between Cairo, Luxor, Aswan, Alexandria, Port Said & Suez. The views from the train can be wonderful, especially on the Cairo-Luxor-Aswan and Cairo-Alexandria routes.
There is no links into other countries using the train, but there are busses - for example from Cairo to Jordan, or into Libya - and there is also the ferry option, from Egypt to Venice etc.
Check out www.seat61.com which is a fantastic site all about travel, especially trains. almost 11 years ago
Egypt National railways runs an extensive network of trains all through Egyptian cities you can look at the linke below where you can get access to a details of the train schedules, distances between all cities
http://www.egyptholidaysdirectory.com/listing/guide/train-travel almost 11 years ago