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Having been to Tokyo, Singapore and Seoul, I can categorically say that Seoul is not in the same league as the other two. Having said that, all three are far and away cleaner than my city of Melbourne, Australia, which has taken an absolute dive in the last 15 years (I've been studying and working in the CBD for 40 years).

Seoul has the problem of regular sewage smell overall.

Holy crap -- I have posted so many times today and I forget to mention Singapore (and Hongkong). Hat tip to you, sir/madam. Singapore's subway is very clean. In my experience, the total system load is way higher in Hongkong, but they do a tremendous job keeping it clean.