I love the U1 line in Berlin. Uhlandstrasse Station is old and the cars are old but the entire thing has so much personality. The seats have little brandenburg gate patterns on them.
My favorite Sbahn station in Berlin is Hackescher Markt. The wooden ceiling, the light fixtures are industrial retro, the filigreed iron posts are beautiful. I have just stared at that station's architecture.
The M1 line in Budapest is one of the oldest existing lines in Europe. It is still very useful, but the stations are charming, with wooden cabinets, scroll work, etc. The trains themselves are throwbacks with interesting lighting inside and manual doors that are fun to open.
The Strassenbahn in Vienna has beautiful signage and some retro trams that wind around the old town.
The Yurikamome Line in Tokyo that goes over the Rainbow Bridge and onto Odaiba. I sat in the front car and the view is amazing as you do a loop and then over the bridge and through the Odaiba modern buildings.
The Metro signs in Paris are in a league of their own. Same with London for the Tube signs and logos.
Some of DC's stations are wonderful architecture. I have only seen pictures of some of the wonderful stations in Russia and former Soviet states.
Miami's Metrorail when you zoom over Miami River at night and all the buildings are lit up for Christmas.
I might be a little obsessed with metros.