The number "12-25" (the date of Christmas) appears throughout the film: the number on the key ring, the cab fare (12,250 yen), a stopped alarm clock, the address in the newspaper ad, the cab license plate.
Toward the beginning of the movie, when the trio passes by a convenience store, in the background you can see the theatrical posters for Perfect Blue (1997), Millennium Actress (2001), and Tokyo Godfathers itself. All three films were directed by Satoshi Kon.
In this film, buildings that look like faces appear in over a dozen scenes, sometimes representing the feelings of the characters. Satoshi Kon describes this in his "Tokyo Godfathers Miscellaneous Notes" as follows: "When I bought my new digital camera, I started taking pictures of such 'faces of the buildings' for fun, but I thought it would be a shame to let it end up as just a hobby. so I decided to use them in this film as symbols of the pantheistic gods, the eight million gods that have existed in Japan since ancient times."
The name of the yakuza boss that the protagonists saved is "Ota", the same name that was written on the grave where Gin got the sake in the previous scene, and since Ota later states in the conversation in the car that he went visit his father's grave.
This shows that the sake that Gin stole and drank was actually Ota's offering to his late father.