- Main article: Ikegami Tsushinki
A company known worldwide for its TV cameras and other broadcast equipment, Ikegami Tsushinki (池上通信機) dabbled in arcade games in the early 1980s. Two Nintendo arcade games have been confirmed to be worked on by Ikegami, but there may be more. One of those games was Donkey Kong, on which Ikegami did the programming. A legal battle with Nintendo over the source code came later. Ironically, Ikegami also worked on Sega's Donkey Kong-esque Congo Bongo.
aka Iwasaki Electronics, Iwasaki Engineering
Kyoto-based Iwasaki Giken (岩崎技研工業) was a subcontractor responsible for disassembling and reverse engineering the original Donkey Kong as Nintendo wanted to make a sequel, but did not have access to the source code that was programmed by Ikegami Tsushinki. This led to Ikegami filing suit for copyright infringement in 1983, claiming it owned the original code.
Iwasaki Giken may have also played a role in the establishment of Intelligent Systems. 
- Soccer (FDS/NES)
Joint venture of Nintendo, Dentsu, and Dentsu subsidiary Dentsu Prox (51% Nintendo, 49% Dentsu and Dentsu Prox) established in April 1991. The Nintendo-Dentsu Game Seminar held from 1990 to 1992 may have been connected with it. Hiroshi Ikeda of Nintendo was the president. 
This article in English only mentions Nintendo and Dentsu, not Dentsu Prox.
- Main article: Pax Softonica
aka Pax Softnica
Frequent subcontractor to Nintendo.
Osaka-based SRD (エス．アール．ディー; Systems Research & Development) was established in January 1979 and is headed by Toshihiko Nakago. The company's game division is located at Nintendo's main office in Kyoto and has worked with Nintendo on many games over the past 20+ years.
SRD also develops and sells CAD software.
- Zelda no Densetsu: The Hyrule Fantasy / Legend of Zelda, The (FDS/NES/FC) (programming)
- And more!