Las Iguanas on the South Bank is right next to Hungerford Bridge, which offers some spectacular views on the underside of the Networkers and and plenty of noise to enjoy from accelerating MetCam sets. Can be very noisy as there is a set of points right next to the seating area though. Not a very romantic spot mind, definitely wouldn’t try having a date there.
Not a cafe or bar, but a picnic on the hill of Brockwell Park in South London offers great views of trains going through Herne Hill. Not so exciting nowadays, but I remember as a kid watching the long Eurostar’s stretch across the landscape past the houses and gardens. The Lambeth Country Show (if anyone knows of it) seemed much better back then!