The Bilbao museum fits spectacularly with the site, and not through pure serendipity but by design. The transformation makes sense, follows naturally, as the building and the surroundings work as a whole. Where else does that happen, I have to think.
I haven't seen it personally, but some pictures of Frank Lloyd Wright's Falling Waters building show a stunning link of building and site.
Bernini's elliptical colonade that forms the piazza in front of St. Peter's at the Vatican is a transformative structure, enfolding the immense space. The surrounding neighborhood was later demo'd in large part when Mussolini cut a swath through it for a street to this piazza, commonly known as St. Peter's Square. Prior to that, the immense space was a surprise obtained by walking through the relatively narrow rather jumbly streets of the borgo.
http://www.romeartlover.it/Vasi27z.jpg