The line along the the left bank of the Rhine has got to be a favourite even though I've only travelled on it once. I went on the EC7 service from Cologne to Chur, formed of a DB 101 and about 7-8 SBB international coaches. As the train leaves Cologne Hbf you glimpse lots of industry on either side of the coach: steel works, lignite mines, power stations etc. It's a bit like the West Midlands or Sheffield prior to the 1980s. Then the line reaches the left bank of the Rhine. If you're lucky enough to sit on the left hand side of the train, be prepared for some awsome vistas of the Rhine. You'll be able to see castles, meanders in the Rhine and so forth.
There are several lines in Switzerland I can recommend including:
Basel-Zurich. Not the most scenically interesting but the initial 5-10 minutes from Basel is unusual since the line climbs quite steeply. Believe it or not, the train even carries on accelerating such is the drawbar HP produced by the SBB loco. (Again, this was on the EC7, but the DB 101 had been replaced at Basel by a SBB Re420 due to the change in direction and different power supply)
The Bernina Express (train that runs from Chur-St Moritz-Tirano). On the Albula line the train hugs the mountainside, ascends/descends a few spiral loops and passes over the 65m high Landwasser viaduct. The Bernina Pass section, on the day I travelled over it, was quite ethereal when the train passed over a plateau without much vegetation because of the fog!
The Glacier Express: it's one of the top 10 railway journeys in the world. No further words are really necessary
Chur - Klosters: Although the line carriers on to Davos Platz I only had time to travel as far as Klosters. Although the line is less scenically interesting than the Albula line since it travels along the floor of a valley, the train picks up speed remarkably quickly which I found quite exciting. Also despite the lack of tilting ability, the train hit some reverse curves at pretty high speed.
Closer to home;
Epsom - Waterloo, especially from Motspur Park onwards. When I was a kid staying at my grandmas in Ewell, I used to do this journey a lot. Back then I loved it although I do find it a lot less exciting now. Basically, I loved the hum of the traction motors of the 455 as it left Motspur Park. Next the train would pass under the SWML at Raynes Park (If I was lucky I'd see a train on it) and ascend the 1-in-25 to the Epsom line platforms at Raynes Park. Then the driver would open up the throttle to Wimbledon, on the right hand side of the train I'd see a 421/423 or 442. Adding even more variety I might see a 319 on a Sutton loop service before the train plunged under the office block over the tracks before stopping at Wimbledon. I'd be really excited if I saw a C or D stock train in the LU platforms before the train left and hit 60 over the flyover past Wimbledon depot.
The St Ives branch line. Definitely one of the most scenic lines in the country.