Kirkstall Abbey, Skipton Castle (briefly....if you know where to look), Pendragon Castle, Lammerside Castle, Brough Castle (on a clear day) and Appleby Castle are all visible from a Leeds-Carlisle train.
Carlisle Castle and cathedral are very close to the WCML to the North of the station.
Lancaster Castle and cathedral (or is it still officially a priory church?) are very close to the North end of the station.
Lincoln Cathedral is visible about 15 miles away - if you know where to look - from the ECML North of Newark, as it is from all four lines entering and leaving the city itself.
Conisbrough Castle is visible from the Sheffield-Doncaster line.
Sanqhuar Castle is visible from the G&SW line.
Kilchurn Castle is visible from the Crianlarich-Oban line.
Old Inverlochy Castle is alongside the Fort William-Mallaig line.
Thirlwall and Prudhoe Castles are visible from the Newcastle-Carlisle line.
The ruins of Furness Abbey are alongside the Dalton-Barrow line (propped-up with lots of bright red scaffolding last time I passed).
Stokesay Castle - mentioned above - is definitely visible from the Marches Line, as are Ludlow Castle, Hereford Cathedral and Abergavenny Castle.
Loughor Castle, Kidwelly Castle, Llansteffan Castle, Carmarthen Castle and Pembroke Castle are visible from the Swansea-Pembroke Dock line.
Stafford Castle is (briefly) visible from the WCML.
Chester Cathedral is also visible from the line alongside the race course, as well as the castle.
Both Liverpool cathedrals are visible from the Runcorn line....and probably the Chat Moss line too.