Former Capcom big wig Keiji Inafune is starting two new game development companies: Comcept and Intercept. "Comcept" is a combination of "computer" and "concept". Oddly, "Capcom" is a shortened version of "capsule" and "computer".
So Capcom comes from Capsule + Computer.
I was always under the impression that it came from Captain + Comando, from their arcade game, although something never made sense in that reasoning as they had made many other games before that one.
I'm actually satisfied with finally clearing that one out.