This is an old page. The current version can be found here.
Despite setting zonal fares a few years ago, the fare structure for rail journeys is still incredibly complex. TfL have a series of pages on their website which describe the various scales in great detail. Here is a link to the page describing National Rail fares. On the right hand side of the page are links to the other pages in the series for TfL rail fares, buses and trams, river boats and the indispensible single fare finder. In an effort to simplify some of the information, this site now hosts a page with all the daily caps and travelcards for zones 1-9.
The single fare finder is the bible for finding the fare between any two rail stations in the Oyster area. When you select your start and end stations and type of fare (adult, child, etc) it will display the fares for the default route and any alternative routes below. You no longer need to click on an “Alternative fares” button. It is really important to describe your journey the right way round because the times when peak fares apply can be different depending on the direction of travel.
There is only really one flaw with this utility and that is that it doesn’t describe what it thinks the default route is. In most cases this doesn’t matter, but it can cause confusion in some cases. You also need to be careful when selecting stations which are split in two but with the same name (eg Lewisham NR and Lewisham DLR). The default route from Richmond to Lewisham NR is via Waterloo and Waterloo East while the default route from Richmond to Lewisham DLR is via the District Line and the DLR. The latter also offers a cheap roundabout route avoiding zone 1 via Overground, Stratford and the DLR.
Finally, a little bit of explanation about the different scales for rail journeys. Outside of zone 1 there are only two scales, one for exclusively TfL-Rail (although some of these fares differ on the lines out of Liverpool Street) and one for National Rail (including mixed NR+TfL). If the journey includes travel via zone 1 then it becomes a little more complicated. In addition to the two scales already mentioned, the mixed travel includes an additional surcharge, currently £1.60 peak and £1.50 off peak for adults. Note that this applies to any mixed journey that goes through zone 1, even if the bit within zone 1 is exclusively National Rail. And just to complicate things a little further, if you switch between National Rail and the Underground at either Vauxhall or Elephant and Castle you can sometimes get a cheaper fare where the NR bit ends in zone 2 and the Underground bit is only in zone 1.
Please see the definitions page for an explanation of the lines included in TfL-Rail and National Rail.