The Back to the Future trilogy was created, produced and written by Bob Gale and Robert Zemeckis. Reasons for selecting certain names for people or places have been mentioned over the years, and some names can be found elsewhere in film lore.
Bob Gale noted that Marty's mother, Lorraine Baines McFly, was so named at the request of Universal Studios President Sid Sheinberg, who didn't like that Marty's mother would be named "Meg". According to Gale, Sheinberg said "Name her Lorraine!", and that "Coincidentally, his wife's name is Lorraine." Sheinberg was married at the time to Lorraine Gary. 
According to Bob Gale, Doc Brown's first and middle name (Emmett and Lathrop respectively) were selected "because Bob Zemeckis and I [Bob Gale] thought they sounded good, and were somewhat out of the ordinary, thus creating a good contrast to the common last name of “Brown.”" 
In their question session at USC, Gale and Zemeckis were in agreement that Marty's name was not drawn from the popular 1955 movie Marty (in the first drafts of the film, Marty went back to 1952 rather than 1955). Coincidentally, the heroine of the film was a schoolteacher named Clara, and the title character (played by Ernest Borgnine) was a man who finds his true love after resigning himself to a life of loneliness. In a 2003 interview, Gale was asked "How did you decide the character Marty McFly's name?" and he said that he and Zemeckis "knew a guy named Marty who was a production assistant on Used Cars and it sounded like a good, all-American name. And Zemeckis just said, 'How about McFly?'" http://www.boxofficemojo.com/features/?id=1258&pagenum=all. The production assistant referred to was Marty Casella http://www.imdb.com/title/tt0081698/fullcredits?ref_=tt_cl_sm#cast.
Although "McFly" is a fictitious name, it was used previously in the 1967 comedy The Honey Pot, a film starring Rex Harrison, Susan Hayward, and Cliff Robertson. Robertson's character was named "William McFly" . The Honey Pot was based on tbe 1959 Frederick Knott play, Mr. Fox of Venice (as William MacFly), which adapted Thomas Sterling's 1955 novel The Evil of the Day (as William Fieramosca, "literally 'Proudfly'"), which in turn was based on Volpone, a play that had been written in the 17th century by British playwright Ben Johnson. The character names in Volpone had been drawn from Italian words for various animals, including "Volpone" (big fox) the nobleman, "Voltore" (vulture) the lawyer, "Covino" (raven) the merchant, and... Volpone's servant "Mosca" (the fly). Robertson's character, first on screen with the McFly name, shares a name with William McFly, Marty's great-grandfather and the last McFly to appear on screen in the trilogy.
D. Jones, who hauled manure in 1955, was reportedly named in honor of unit production manager Dennis E. Jones. In the third film, the 1885 manure hauler (A. Jones) was named for Jones's son, Arlen Jones.
- USC session, DVD-1, 18:00 minutes