Bond drinks Jack Daniel's in the novel On Her Majesty's Secret Service (Ian Fleming, 1963), the novel You Only Live Twice (Ian Fleming, 1964) and in the movie GoldenEye (1995).
In the movie GoldenEye Bond is drinking Jack Daniel's whiskey with M in her office. The bottle can be seen on the counter, at around 49 minutes into the movie.
The name is not mentioned, but the drink is only referred to as 'bourbon', which technically is incorrect since Jack Daniel's is a Tennessee Whiskey, produced in a different way than a Bourbon Whiskey: Tennessee whiskeys are charcoal filtered for several days.
M: Would you care for a drink?
007: Your predessesor kept some cognac in the top drawer of...
M: I prefer Bourbon. Ice?
In the novel On Her Majesty's Secret Service, Bond pours himself "a stiff Jack Daniel's sourmash bourbon on the rocks and added some water" (Ian Fleming, 1963), when he is in Draco's office.
In the novel You Only Live Twice, Bond orders a "pint of Jack Daniels" (Ian Fleming, 1964) with a double portion of eggs Benedict in his hotel room in Kyoto.
About Jack Daniel's
Jack Daniel's is a brand of Tennessee whiskey that is among the world's best-selling liquors and is known for its square bottles and black label. It has been prominently featured in movies, songs, and novels, and is strongly linked to rock and roll, country music, American biker culture, Jimmy Page, Frank Sinatra, Keith Richards, Lemmy, Nikki Sixx and Slash.
Thanks to Terrence for the alert