The bus Conan and his group were on in the beginning of The Man Who Fell Slowly was traveling to the Beika City Building, the site of the climax of this movie.
In Night Baron Murder Case (Suspicion Part) (1997) Akiko Sayama was watching a movie on TV where there was a bomb on a skyscraper, referencing this case.
The TR Beika Line in real-life is JR Yamanote Line and the JR Tokyo inspired from JR Yamanote Line 205-0 series set 30.