Here are a few of them that I travelled myself and that I can recommend.
Belgium, my home country : basically all lines along and south of the Sambre and Meuse rivers.
If a choice must be made, Liège to Luxembourg would be mine.
France : both lines crossing the "massif central", i.e. Clermont-Nimes and Clermont-Beziers.
Both are threatened, so hurry up.
Spain : The long-distance train (not high speed) Barcelona to Malaga. And also the short stretch between
Antequerra and Granada, although this one is getting HSLized so I don't know its current status.
Italy : Naples to Palermo - sit on the right side to look at the sea - with the Messina strait crossing
Romania-Bulgaria-Greece : The international train Craiova-Sofia will take you in a 80 years time
machine, the 3-car train being hauled by a shunter at 60 km/h max to the new Calafat-Vidin bridge
on the Danube river, over a line that looks much like a german Nebenbahn of the 30ies. Once in Vidin
your carriage will join a domestic train on a very scenic trip to Sofia. And then (after a night in
Sofia) the scenery on the way to Thessaloniki in Greece is even better !
Greece : the central, not yet modernized part of the line between Thessaloniki and Athens.
Turkey : the line between Malatya and Tatvan, and the Van lake crossing on the ferry.
Mongolia-China : going uphill out of Ulan-Bator, and then the crossing of the Gobi desert.
The bogie exchange at Erlian in the middle of the night. And then the chinese part with some
spectacular mountain and river scenery on the way.
Israel : the line from Tel-Aviv to Jerusalem, which will probably be partly abandoned once the
new HSL (or so they name it, but il will be 160 km/h only) is put in service.