I think Berlin has an amazingly comprehensive transit system of S Bahn, U Bahn, Trams, etc,
Tokyo was intimidating to figure out at first, but I found it a wonderful system. But I needed something like Google Maps to figure it out.
Its a puzzle to me, and I have to try to get around by subway/tram no matter the city. Amsterdam has my favorite tram system. Vienna has fun trams, Budapest has some of the steepest deepest escalators I have ever been on. They make me dizzy.