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 8 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 8 years ago