A few comments on the parts I know myself.
As said previously, the section Clermont-Ferrand Nimes (Ligne des Cévennes) is very scenic and a masterpiece of engineering (many viaducts and tunnels), especially between Langogne and Grand-Combe. Unfortunately, the line has suffered of low maintenance and has many speed restrictions (down to 30km/h).
Veynes Grenoble (Ligne des Alpes) is also a highly scenic route with some beautiful viaducts. X73500 railcars have large windows to enjoy the trip. As far as I remember, best views are on the right when running northward.
Genève Lausanne : not the most interesting part along of Lake of Geneva. The line is never close to the lake shore. The most interesting section is Lausanne Vevey (- Montreux). At Morges, you may have a glimpse on the narrow gauge BAM (left side when going toward Lausanne), and possibly standard gauge wagons on narrow gauge bogies.
Paddle Steamer on the lake, always a good experience. It is worth to pay the extra cost for 1st class to enjoy the landscape on the upper deck. Extra fare ticket for 1st class is available on board.
St Gervais Le Fayet to Martigny : very steep section (90mm/m or 1 in 11) without rack after departure form St Gervais, view on the Mont Blanc massif after Argentière, impressive gorges after the Swiss border (La Chatelard).
Montreux Zweisimmen Spiez : my preferred swiss route ! At Montreux, 3 different gauges in the same station (standard for CFF, metric for the MOB, 80 cm for the MGN). At Chamby station, you can see the museum railway (Blonay Chamby) on left side. At Montbovon, connection (on left side before the station) with a street running railway (TPF). Views not to miss : 1) the panoramic section between gruben and Schönried 2) the aerial view on Zweisimmen station (2 gauges, standard and metric) after Oechseite.
Göschenen : a night here is pefect for trainspotting on the station platform, on the Gothard line. Will you really sleep this night ?
Andermatt Disentis Chur Samedan Tirano : very famous fantastic routes ! Before Filisur station, don't miss the landawasser viaduct, wich is easy to see from the train due to the tight curve on the right. But it is currently covered with scaffoldings for heavy maintenance works.
A last thing about Swiss trains : according to your liking, you can choose between panoramic trains (Golden Pass, Glacier express, Bernina express) or standard trains. Panoramic trains offer excellent views on the landscape and have air conditioning but are often crowded with tourists, while in standard train you have chance to have trains with opening windows an to travel quietly with locals.
Verona Fortezza : the Trento Male narrow gauge railway may be seen a couple of times from the main line, after Trento station. Fortezza San Candido is a highly scenic route, where you can hardly guess if you still in Italy or already in Austria.
You finally hesitate between Golden Pas and Centovalli ? I couldn't choose between these 2 routes...
Éric