In No Hero, Carrick Masterson had been able to control the world since the sixties. He was responsible for having Nixon only stay one term in office, the Great Iran Oil Fire, and the destruction of South Africa.
The kids in Bryan Lee O'Malley's Lost at Sea decided to head for another diner when they couldn't find a Wendy's, because "sometimes it's good to give your money to somone other than The Man". Cue laughter.
The second issue of the Black Dynamite comic sees the titular hero taken in and offered a job by a bald (white) individual who, when asked who he was, answered "I am The Man". More specifically, The Man is the representative of the Illuminati, the (predominantly white) elite who secretly run the world.
Jack Black's character in School of Rock rambles about The Man, prompting the kids to stick it to The Man. This leads to one of the kids telling the principal that "[she's] the Man." She thinksit's a compliment.
Captain Industry, the Big Bad of Defendor. Subverted, though, as in reality he doesn't actually exist, the protagonist confused a comment about his mother being "killed by the captains of industry" for his mother being "killed by Captain Industry."
In A Calculated Magic by Robert Weinberg, protagonist Jack Collins poses as an agent of The Man, who is a very real figure of modern origin among the living legendary and mythological beings that populate the Logical Magician series of novels.
The infamous "Big Brother" in the novel and movie 1984.
Walker from Simon R. Green's Nightside books. At the end of The Good, the Bad and the Uncanny, John Taylor is maneuvered into taking his place.
Randall Flag is the source of all evil in the books by Stephen King. Any truly evil enterprise is linked to him in some way.
Dave Gorman's documentary America Unchained was all about trying to tour America whilst avoiding what was called (at least in the book of the series) "The Man(TM)"- that being the big chains of shops, gas stations, motels and such, in favour of smaller, independent "mom and pop" businesses which were becoming harder to find.
The Illusive Man in Mass Effect 2, played by Martin Sheen. He communicates with Shepard to provide them with info via hologram and is always shown in dim light while smoking a cigarette and/or drinking. His name and backstory are only explained in a tie-in comic; none of the characters, including his right-hand-woman Miranda, have any idea where he came from or how he got where he is. All they know is that he has staggering resources and big, big plans for his species.
The Half-Life "G-Man" is always lurking around in the backscenes, armed with a briefcase that could contain anything, dressed in a perfectly anonymous suit. He may take a train to the opposite of your direction, he will still be at your destination before you.
In Alpha Protocol, Henry Leland thinks he's The Man. Potentially, however, Mike Thorton can become The Man through careful manipulation and control of his contacts.