I suppose we can include a couple of DLR items.
Most blatant was the initial Canary Wharf station. Between starting to build the initial DLR and its completion the vast Canada Square development was agreed, for which the wayside station was no longer relevant. On opening day it was already half demolished again. Due to a feature of the automatic control system trains still stopped at that position on the viaduct without opening the doors, although the canopies and access steps had been part-removed. Eventually it was completely removed, and the core of the current station built around it.
The initial system also had a triangle junction between its three arms. Public trains never ran between Tower Gateway and Stratford so that side of the triangle was never used apart from ECS workings. Eventually the tracks were removed, although the viaduct structure remains.
For a system which only first opened in 1987, 35 years ago, it's amazing how little of the original station structures on that initial system remain, the vast majority have been rebuilt, often more than once, to be unrecognisable now.