Each regeneration of The Doctor is represented by a different coloured tube line. The stations are the baddies he meets on his journeys, with interchanges where more than one Doctor battled a particular enemy - Doctors two and three met The Ice Warriors, so their lines cross there, and it gets very complicated at the Dalek and Cybermen stations.
You can click on each Doctor and see their line with companions as zones travelled through, just like the maps inside tube carriages, and everything's clickable - if you want more info on something it'll link you to the relevant page on the DW wiki.
And now we know why The Doctor keeps appearing in London; the River TARDIS runs right through it.
A few notes on the map from creator Crispian Jago:
The map does not include characters from the associated Doctor Who films, books, comics, animations, and spin-off series such as Torchwood or The Sarah Jane Adventures. Historical characters visited by The Doctor are not depicted on this map. Reappearances of The Doctor in past regenerations are shown on the map as hollow, rather than solid lines. As a Doctor Who fan by inference you are probably also a pedant and have therefore noticed all sorts of continuity errors and mistakes such as some characters appearing on my map out of sequence. This is of course a restriction of my chosen format but you have to expect some sort of weird paradox shit once you start messing around with the space-time continuum, it's just one of those things. Get over it.
Click here to avoid getting lost in time or space - http://www.crispian.net/DoctorWho/DrWh…