Actor Allusion: "I'll miss you, Chihiro. Your best friend, Rumi." (In the Japanese version, Chihiro was voiced by Rumi Hiiragi.)
Executive Meddling: With a rare positive spin and happy ending. After the lackluster box office showing for Princess Mononoke, Disney executives were hesitant to move forward with more of the Studio Ghibli films they'd bought the rights for. Castle in the Sky had been dubbed and shown up on the film festival circuit, but no proper release date was announced, and it seemed like the other Ghibli films would be lost in Development Hell. The happy ending? John Lasseter, then the head of Pixar, stuck his neck out to push for Spirited Away's production and release in America. Lasseter's championing of the film, and its eventual Oscar win, was the impetus for the eventual release of the rest of the Ghibli catalog on DVD, as well as distribution of future Ghibli films.
On some editions of the DVD, John Lasseter appears before the movie begins to gush about how wonderful Spirited Away is. There's even footage of him with his arm around Hayao Miyazaki!
John: Miyazaki-san, the world; the world, Miyazaki-san.
Reality Subtext: Devoted environmentalist Miyazaki included a bicycle getting pulled out of the polluted water spirit after a clean-up group he was part of actually did find one in a river.
When Chihiro accidentally steps on a Soot-Sprite, the Boiler Man does a "cut the line" routine with her. In Miyazaki's time, this was a "cleansing" ritual that kids performed among each other when one of them accidentally stepped in poo. Much to Miyazaki's chagrin, he had to explain this to Chihiro's young voice-actress!
The translation staff had trouble with the gesture as well, until someone realized that it was thematically similar to a "cootie shot" schoolkids would use.
Throw It In: John Ratzenberger's character's little song was entirely improvised for the dub.