Dr. Gari-Gari - Puss n Boots

Dive Man - Mega Man 4

Drill Man - Mega Man 4

Dust Man - Mega Man 4

Didalos - Boss in Final Fantasy 6

Dullahan - Another boss in Final Fantasy 6

Dino - The Flintstones: The Rescue of Dino & Hoppy

Dr. Doak - Goldeneye 007

Daffy Duck - Daffy Duck: The Marvin Missions (and other Looney Tunes games)

Donald Duck - Donald Duck: Goin' Quackers (and other Disney games)

Darkwing Duck - Darkwing Duck (NES)

Drumstick - The rooster in Diddy Kong Racing (isn't Drumstick kind of a morbid name for a rooster?)

Dan Danger - Space Station: Silicon Valley

Dale - Chip n Dale Rescue Rangers

Duey - DuckTales (of Huey, Duey, & Luey)

Dragon Lord (aka Draco Lord) - Dragon Warrior