My three favourites, in alphabetical order, are Hong Kong, London and Paris. My particular dislikes are New York (efficient but dirty and horrible) and San Francisco (badly maintained and filthy).

Obviously a subway system has to get the basics right (speed, connectivity, adequate comfort, convenience etc.) but increasingly I find ease of payment really becomes important. Here London is streets ahead (completely contactless throughout the system, including bus with fare breaks and caps fully integrated), Hong Kong is good but you have to rely on Octopus and busses are different. Paris has fallen behind with the Metro, bus and RER all on different systems.