I have a few places i like to head to each time im in London.
Bethnal Green (Be warned, the tube station is a short walk from the mainline station) is a great place to capture trains that are going in or out of Liverpool Street Station. if you stand at the London end of the station you can also get a good picture of trains coming round the corner off Hackney Downs
Royal Oak is a stones through away from paddington (You can actually see paddington station at the London end of Royal Oak) its all in the open for the best pictures (So take a brolley), but this is great as the HST's crawl in and out and you dont have to walk up and down the platforms. Also, it is not a manned station, so you dont get hassled by the "Badge brigade" hassling you over what you are doing
East Croydon, its a bit of trek out of London, but its a very busy station which is aminly served by soutern units. However, right out the front of the station is the croydon tramlink, and about 20 yards down the hill is a traffic light junction which allows for some nice shots of trams entering into the east croydon tram stop
one final thought (As im not sure if you want light rail tuff as well). Poplar on the DLR is a nice place for pictures. it has a depot (Which is usually empty during the day but you might lucky and see the shunter they have on site) but a lot of the lines converge here and if you have a good enough camera even the ones that divert for canary wharf can be photographed (Quite nice as they disappear into the buildings!)
either way, have a great time and if you find any new places on your travels be sure to tell us all !