I use a copy of the Project Mapping maps on which I've converted the lines to black and white, and then coloured them back in accordingly using photoshop. I use red for lines I've travelled over and stations I've travelled from, orange for lines I've walked or stations I've merely visited, and sometimes add some green for future booked journeys.
It works well for me, although it's hard to see the whole country at once, as I can easily switch between colours and all stations are marked, including London Underground and some metro ones. I have been tempted by a book, but it's less accessible and a pain to update when they make changes to the network, whereas I can usually splice in a new part digitally without redoing the whole thing. Easily added in little semi-relevant extras such as the Gosport-Portsmouth Ferry and the Emirates Airline cable car too. Not looking forward to Crossrail coming into existence though...