Took me a while to settle on a headline.
Via Rolling Stone:
"I would say the film's biggest legacy was that it was an introduction to the world of two extremely gifted filmmakers: [screenwriter] Charlie Kaufman and Spike Jonze, whom I hold in great esteem," Malkovich tells Rolling Stone. "In my mind, they're visionaries who have gone on to do some of the most excellent work in American movies for a long time.
"But [the legacy] for me, not so much," the actor adds. "I mean, in modern culture... [Long pause] It's kind of like if you get a blowjob from the wrong person, then your life becomes a blowjob. So Being John Malkovich always has to be referred to in some allegedly clever or ironic or snarky way." (Source)
So there you go. Also this:
"We [Charlie and Malkovich] were walking down the street in New York after I met him the first time. It was not long before we started shooting and he sidled over to me and said, 'I just want you to know I'm a big fan.' And I said, 'Well, thank you, Charlie, but I read the script, so you don't really have to do that.' And he kind of snorted."
Thanks to Sarah!