I see how everybody's approaching the graphical shortcomings of cave story with a lot of liniency because pixel made this whole game by himself, and that's fine. There's also the issue that when you do pixel art for fun, and then you shift to doing pixel art for a game, you have to do tighter scheduling and a lot more utilitarian than artistic decisions that make the art look worse, but you can make it faster and more consistent. For example, I rant about color unification in pixel art. Well, in game art? It makes more sense to have mostly separate ramps for remapping or just for neatness. Not everybody works with a universal 256 colours palette, that is premade before art. And so on for colourcount choices and how much time one spends on a single animation... if you take the top hobbyist pixellers from here and make them make a short game each, nobody will make art on the level of their hobby stuff, they'll all deteriorate to 32x32 tileage we've seen before and megaman-clone gameplay, probably.
I don't find the art in cave story amazing or even very good. But it serves it's purpose and the game plays very well. Artistically it's sometimes charming. I can't speak technique for this, as there isn't much of it. It frankly amazes me how some people in this thread have apparently pulled techniques out of thin air to talk about pixel's work, whereas I see fast, non-AA'ed cell-shaded game art.