Studying kanji is not an easy activity outside Japan. The only appearance of the characters is within the confines of the study arena - there is no incidental reinforcement by the appearance around you that you get studying a language in it's own county, for example on TV or in on-train advertising.
When studying the kanji in isolation for it's basic meaning, as I do when consciously trying to learn new kanji, I find the meaning and the standalone 'kun-yomi' reading tend to stick more readily than the various compound 'on-yomi' readings. I would imagine this is because in many cases, because of my limited number of total kanji, many of the compound meanings are quite difficult for me as I may not know the other kanji in the compound. Without a mental 'hook' upon which to hang the new word, it falls away.
However, for me, one of the most noticeable improvements in my Japanese comprehension each time I return to Japan is that I can read more and more signs on the station maps; I can both find my way around the maps more quickly (now sometimes more quickly than my wife too!) and I get a feeling for the name's meaning. This has a knock on effect as I learn more on-yomi, or compound readings, for each character. Crucially, this also means that I have a 'hook' upon which to hang more new meanings. Since I know the whole word from navigating the rail lines, and I know some of the kanji, I remember the pronunciation of otherwise unknown kanji.
Take for example 上野 （うえの or Ueno). 上野 is the terminal station for the Joban Line in to Tokyo, and a major station on the Yamanote Line that rings Tokyo. The first character in the title, 上, is one that you learn very early on and means 'up/above'. The second character, 野, is one I don't know yet, but which JDic tells me means 'field'. So I now know 上野 roughly translates as 'upper fields' which is consistent as it atop a small hill I guess.
A second example would be with the even better known 東京, a little place you may have heard of, known in English as Tokyo. The first character here, 東, means 'East', but on its own is pronounced ひがし or 'higashi'. It frequently appears as this as often a town/area has more than one station and the location is often the way to distinguish them: see Nishi-Funabashi, Funabashi and Higashi-Funabashi stations on the Chuo/Sobu Line for example (West-Funabashi, Funabashi and East-Funabashi respectively). In the case of 東, getting familiar with the compound pronunciation, とう or 'tou' is useful, and opens the way to further understanding - for example getting to realise that the 'Touhoku' region the guidebooks refer to is simply 東北, or 'East North'.
Of course, you may make all these connections yourself during your study. But equally, like me, you may find that being presented with more contexts for the isolated characters presents ever more ways of creating the links and meanings to help secure understanding.
And it goes without saying that learning the names of train stations does have an additional and more direct benefit beyond learning kanji - you can just get around more easily.
With these learning and practical values in mind, I have started to create flashcards for stations around Tokyo at Flashcard Exchange, one of the better generic study tools I have found on the web. I like Flashcard Exchange because it allows you, after making a small one-off payment, to deploy the Leitner system, a methodical approach to flash card study that focuses effort where it is needed, using the idea of spaced repetition to help move new knowledge in to long term memory.
So far I've managed just the Yamanote Line, but I think I'll try to add some the other JR and Metro lines when I get the chance.