Maynard G. Krebbs
According to Maynard, the G was for “Walter” (“the G is silent”).
Pavel Andreevich Chekov
If he’s from Texas, it’s gotta be “Lee.”
Runnymede, “mede” in this case meaning “meadow.”
Christopher Cross Griffin
Julian Subatoi Bashir.
Miles Edward O’Brien.
Christmas Noelle Snow (“Chrissy”)
Father John Patrick Francis Mulcahy was sometimes John P., other times John Francis.
Benjamin Franklin Pierce
BJ Hunnicut (named after his mother Bea and his father Jay)
When you have that many names, you can afford to skip a few now and then. 
My Little Pony: Pinkamena Diane Pie. Which is pretty weird since it’s the only human sounding name in the series.
I wonder if it’s a deliberate shout out or just a weird coincidence that Pinkie’s middle name starts with D and so does Luffy’s in One Piece.
Stanislaus Tadeusz Wojciehowicz (“Wojo”)
Leroy Jethro Gibbs, from NCIS
Timothy Farragut McGee, also from NCIS
Michael Casimir Stivic
Was he ever called John Francis? It was “John P.” in the pilot, but usually just “Francis” in the rest of the series, when he didn’t use the full name. The one time I remember him saying the full name was when Radar was leaving; he told him something like, “John Patrick Francis Mulcahy - remember that if you have any children!”
Speaking of Father Mulcahy, how about characters that are called by their middle names:
Lucille Quinn Fabray, from Glee
W. Seymour Skinner, from The Simpsons - however the only time his name appears that way is in one of the “Who Shot Mr. Burns?” episodes (as part of the whole “Burns points to WS, or is it MS” plot point)
And Benjamin LaFayette Sisko
Sheriff Andrew Jackson Taylor - the Andy Griffith Show
Arthur Herbert Fonzarelli - Happy Days
A couple more: Dana Katherine Scully and Fox William Mulder.
Charles Edward Eppes (in Numb3rs)