For example, in the Phantasy Star Online Intro song, the main melody starts to play in 3/4 time, whereas the overall song (and the harmony) remains playing in 4/4 time. (starts after 10 seconds, at the 0:50 mark). Technically, you can probably say it's 4/4 time, or 12/12 time if you want to be silly, but it's clear that the melody and harmony here are seemingly playing with different time signatures, only syncing up every few measures (4 in this case).
Does this have a name or any way it's referred to commonly? I can't really think of any other songs that do it off the top of my head, so perhaps it's not notable enough....