My favourite piece of London's transport is the hand-operated pedestrian
chain ferry to Trowlock Island in Trowlock Way, Teddington. It's about
the size of a single bed. It rocks like a double bed ;-)

Various Charles Holden stations, particularly Southgate at night.

The old passimeter in Arnos Grove.

The "See How They Run" dials in the foyer of 55 Broadway for the six
historic lines.

The silver tubes which stop big trains going into small tunnels at
Barons Court, Finchley Road.

Did they put humps for wheelchair access on certain platforms?

Those lovely escalators at Southwark station.

The Eurostar station at St Pancras and the former one at Waterloo.

The pantograph changeovers at Drayton Park and Mitre Bridge.

The views over the Thames on the District /NLL near Kew Gardens (IIRC
the Thames view is obscured on the Putney Bridge line)

The Bakerloo passes through a shed in both directions between Queens
Park and Kensal Green.

Behind the Marks and Spencers in Southgate you can see the Picc tunnel
entrances, and see how the entrance tunnel is much larger than the exit
one (the entrance is tapered to lessen the sonic boom from trains
entering the tunnel at speed.

The fake houses in Leinster Gardens.

The abandoned open-air platforms at Highgate Station.

The metal hooks for tying up boats set into the pavement of Surrey Canal
Road, revealing that the road is a former canal and the pavements are
unreconstructed tow-paths.

The bridge over Waterloo Road which used to carry the connection from
the South East Lines across the Waterloo concourse.

Deep level shelters.
http://en.wikipedia.org/wiki/London_deep-level_shelters

Escalator cavern at Westminster Station

The Underground entrances set into the corner of the Bank Of England,
and the air grilles hidden in the Greathead Statue in Cornhill. The
Greathead shield which forms part of the passageway to the W&C.
http://www.greathead.org/greathead2-o/JHG3.htm

Thames Tunnel and the Brunel Museum

Old station tiling at Arsenal station saying "Gillespie Road"

Stations with lifts, e.g. Russell Square or Covent Garden.

The old train indicators at Earls Court District Line

The big platforms at Euston and Angel

The tiny platforms at Clapham tube stations