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The Making of Super Mario Bros. 3
Via Press the Buttons, a Nintendo Power feature on Super Mario Bros. 3, and the making of the game. From the post: "It's an interesting little article that has largely been forgotten over the years, as I've never seen any of the little tidbits and factoids in the piece resurface in other places (such as the existence of a centaur power-up instead of the raccoon leaf)."
In general, console programming on all the cart machines was done on a workstation with custom software(I remember reading somewhere that Nintendo used Apple IIs into the early SNES era). They all used assembly, of course. The compiled program was then transferred by data link hardware into some form of memory identical to ROM for test purposes. Debug monitors were also put together by the more sophisticated outfits.
Part of the problem for homebrew developers is that nearly all of this stuff was proprietary, custom-built, and usually became lost to history as soon as the developer folded. None of the systems were particularly HARD to make this stuff for with the right electronics knowledge and some reference material, but there wasn't any getting around it either, which is why 80s game development has such a mystique to it. Nowadays everyone develops with "off-the-shelf" kits and software, so it's substantially less interesting.