In In chapter 11/episode 3 of Barakamon, Naru's face changes into a style very reminiscent of Golgo's to represent how cool and mature she feels after learning how to read katakana.
In Dandadan, Okarun gives Ayase a limited-edition DVD of the first Golgo live-action film as a present, as she has a Celeb Crush on its star Ken Takakura. The chapter where this happened was published shortly after Takao Saito's death.
GTO: The Early Years: Ryuji almost elbows someone who snuck up behind him in the face, who then asks if he's Golgo.
In Lupin III: Part 6, episode 4, an Expy of Duke Todo is one of the dozen assassins at the Cafe.
The manga version of Magical Shopping Arcade Abenobashi has main character Sashi get mistaken for "The Legendary Assassin Lugolgo 12" in the hardboiled world.
It's never remarked on within the show, but Todo regularly gets his coffee at the Mitsuyoshi family shop in Tada Never Falls in Love, seen as a silent customer in the shop. He even secretly snipes a prize at a street fair for Theresa and Tada with a cork gun.
The Battle Cats features a sniper cat, Sniper the Heavy, which is named "Negolgo" in Japan. Using it even activates a combo called "Thirteen." Its true form, Sniper the Deadeye, takes the reference further by being named "Negolgo 31" in Japan.
Saints Row: The Third has the Togo-13 automatic sniper rifle available in one of its many DLC packs. The weapon in question even behaves similar to Golgo's iconic scoped M16 rifle.
at one point.