I've got to disagree with Alavahalf on this one. I used to run a railway station and we frequently had people turning up with train tickets issued by The Trainline.com and similar online companies which weren't valid on any trains at all. Further, many of those companies charge a booking fee.
Every available train fare (other than as below) should always be on the National Rail website:
http://www.nationalrail.co.uk/
If it's not there it doesn't exist. Further, you can book by following the links from that site without having to pay any booking fees.
The only fares which don't always appear on the National Rail site are those offered by the Stagecoach group of rail companies under their 'Megatrain' branding. The relevant companies are Southwest Trains (operating out of Waterloo) and East Midlands Trains (from St Pancras). Their services can be booked here:
http://uk.megabus.com/default.aspx
(That really is the correct link, even though it says 'Megabus').
If you need help in finding the cheapest fares, tell us where you want to travel between, when you want to travel and what degree of flexibility you've got in your travel plans.
Chris