Dr No is barely in, erm, Dr No.
Then how about Waiting for Guffman?
Or Waiting for Lefty.
A couple further ideas:
- The Big Lebowski: The movie is about a slacker named Jeffrey Lebowski, not the “Big” Lebowski, a millionaire with the same name who barely appears in the film.
- Peter Jackson’s The Lord of the Rings trilogy: The title refers to the Dark Lord Sauron, who sets the plot in motion but who appears bodily in only a brief flashback.
And, from time to time (though, again, only briefly), as a giant disembodied fiery eye. 
The entire Thin Man series of movies and the TV show.
The “Thin Man” was not the William Powell character but the person of interest in the first movie.
Waking Ned Devine
The Zodiac Killer isn’t in Zodiac much.
A twofer: To Wong Foo, Thanks for Everything! Julie Newmar
Or is he?
…or she?
The Iceman Cometh
They’re not characters at all, but the title of Glengarry Glen Ross seems like it should be in reference to the name of a character, and I would wager that a huge portion of the moviegoing public assumed that Glengarry Glen Ross was the name of either one main character, several main characters, and/or the name of the real estate firm in the movie. But they’re not. In perhaps a deliberately obtuse move by David Mamet, the title refers to two separate land-development schemes in the plot - one called Glengarry, the other called Glen Ross - which were oddly thrown together to create the three-word title, and which are barely ever referred to in any of the movie’s dialog.
And then there’s The Third Man.
Better Call Saul
Saul doesn’t appear until the season 4 finale
Doesn’t Jimmy make a commercial with ‘Saul Goodman’ in a cheap wig and stick on facial hair in an early episode? I could be misremembering.
The Postman Always Rings Twice
I Love You, Alice B. Toklas
How about Fargo? The story mostly takes place in Brainerd.
The Last of Shiela. Shiela died a year before.
Duffy’s Tavern was an early TV show based on a radio show. Duffy never appears, though he does call occasionally.
Like “Charlie” on Charlie’s Angels.