Iwata was a lead programmer on Earthbound/Mother 2 (my favourite game of all time). The game went through a troubled development and if you trust the impressions of Itoi, the lead designer, Iwata's incredible skills saved the game from cancellation. An Earthbound fan translated a Famitsu interview from Mother 2's initial release where he talks about programming a bit. https://yomuka.wordpress.com/2011/12/24/weekly-famitsu-septe... EDIT: More here: http://earthboundcentral.com/2013/03/itoi-iwata-discuss-moth...
Incredibly, Iwata was still doing some programming work during the Gamecube era in the 2000s. http://nintendoeverything.com/iwata-on-his-super-programmer-...