I have been whistling the Windwaker title theme recently... awesome tune.
As for Twilight Princess, I thought it had really nice music, but it not beine memorable is probably in part due to it not having a playable instrument.
Majora's Mask I only played a couple of weeks ago and I can't remember any tunes from it, despite is having the ocarina and the pipes/drums/guitar. but it doesn't stop me thinking of it as a far better game than OoT.
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P.S. Bolero of Fire is an awesome tune.