One that hasn't been mentioned yet is the former Midland Bristol-Gloucester line under the M4, at what is now Westerleigh oil terminal. The M4 actually still has track under it, the stops being under the south side of the motorway. I've seen p-way machines stabled under the bridge, which is at the left hand side of the photo below.
There can't have been revenue earning railway traffic for very long under this bridge.
Edit: J18-23 of the M4, including the Severn Bridge, opened in 1966, the Lawrence Hill-Yate section of the Bristol-Gloucester line closed in December 1969, so by my reckoning, passenger trains ran under the M4 for 3 years. The Bath branch remained open until 1971, presumably accessed from Yate, so the last revenue earning trains would have passed under the M4 in 1971.