My Mac SE (1987) had a big fan in it, but I think that was as much for the power supply, CRT, etc as it was for anything else. The Motorola 68000 in the thing runs bare in Genesis, Neo Geo, etc.
The Capcom CPS2, also 68000 powered, has a great big stupid loud fan in it, but as far as I know the only purpose is to fill the system with a pound of dust. People unhook the fans (so they can hear the game) and they don't melt or anything. I think the actual 68000 in it doesn't even have a heat sync.