It’s been said that Indiana Jones was inspired by the adventures of Roy Chapman Andrews.
…yet still somehow 68% Phil Hartman. 
And Elvis was based on Captain Marvel Jr.
And Lacey Davenport was based on Congresswoman Millicent Fenwick - my Congresswoman for a while.
I’ve heard Edward Teller, who was more involved with bomb research.
I’ve often thought that the President was based on Adlai Stevenson.
Shakespeare based Falstaff on a real person, named Oldcastle (and called him Oldcastle in some early versions of Henry IV), until the Oldcastle family raised a ruckus, and Shakespeare changed the name to Falstaff. He was a Puritan, which Falstaff sometimes hypocritically pretends to be, and the family objected to his blatant licentiousness. Of course, all the history plays have characters based on real life figures, often with no more relation to history than his plays based on fiction.
In one Loony Tune, Henery Hawk has a father whose name is G. K. Chickenhawk, and who is based on G. K. Chesterton. Coincidentally, Chesterton based his famous priest detective Father Brown on the priest who took his first confession; the story is told in Chesterton’s autobiography.
There’s a tombstone in Liverpool that mentions Eleanor Rigby (though her married name was actually Eleanor Woods). IIRC Paul McCartney denies any conscious connection between this and his song; he named it for the actress Eleanor Bron and for a store he frequented called Rigby’s.
Moriarty was based on Adam Worth, a great art thief and bank robber. Not quite the diabolical mastermind, more like the hardest working man in the heist business.
In a documentary on the DVD of the movie ‘Rocky’, Sly Stallone reveals that the Rocky Balboa character was inspired by Chuck Wepner, an otherwise unremarkable fighter who managed to floor Muhhamad Ali once.
The character ‘The Whammer’ from ‘The Natural’ has been mentioned, but the main character Roy Hobbs was supposed to have been loosely based on Eddie Waitkus, a major league ballplayer who was shot by a crazed fan.
Vetinari in Discworld is almost certainly based on Cesare Borgia.
Alice’s Adventures in Wonderland hasn’t been mentioned yet?
Neal Cassady was the inspiration for “Dean” in Kerouac’s On The Road and “Cody” in various other novels like Visions Of Cody and Big Sur.
And a professor who had lived through that time once told me President Merkin Muffley is clearly based on never-quite-POTUS Adlai Stevenson.
This site about the upcoming On The Road movie shows us the people behind the characters. And which actors are playing those characters. Viggo Mortensen as “Old Bull Lee” AKA William Burroughs, for one…
Foghorn Leghorn was based on Senator Claghorn, a recurring character on the Fred Allen radio show who in turn was partly based on a real person, Governor/Senator/Secretary of the Interior Hoke Smith of Georgia, a big shot on the Chautauqua circuit who really hammed up the southron accent and folksy-ism for public speeches.
The Coen brothers claim in a documentary on the DVD of “The Big Lebowski” that the Dude was based on a guy the Coens knew in LA.
Seinfeld’s Kramer was based on creator Larry Davis’s neighbor Kenny Kramer
J.K. Rowling has said that the character most closely based on a living person in her books is Gilderoy Lockhart. The inspiration was a self-aggrandizing pathological liar she knew who she said is probably out there now telling people he wrote the Harry Potter books but let her take credit.