This reminds me of a link to a site I stumbled upon once that detailed, with screenshots, many of the subdued darker elements of MM, like the scenery, things hidden in the background, etc. as well as the more obvious elements/themes. I know that sounds vague, but does anyone know what I'm talking about? I'd love to check that page out again.
EDIT: Actually, read this one before the other: http://www.zeldauniverse.net/articles/the-stone-tower-why-termina-was-doomed/
http://www.zeldauniverse.net/articles/the-message-of-majoras-mask/
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http://backloggery.com/genesistwilight/sig.gif
http://mlkshk.com/r/3JLF.gif