Well, I don't know if this counts as metaplot (since there was no chronological development of the idea during the product schedule), but...
I ran a Planescape campaign where the identity of the Lady of Pain started as a foreshadow, then a sub-plot, then the big reveal of the campaign. It turned out she was the scorned lover of the big bad demon prince, and there were hints that one of the PCs was her daughter/cosmological twin/metaphysical reflection. I took that one idea introduced in the PS boxed set and ran with it, providing lots of suspense and a mystery the PCs couldn't resist. Lots of fun was had.