When watching Notch code I noticed a lot of code smelly habits, relying on inheritance over composition is one example. But my god his level of productivity and ability to get shit done is lightyears ahead of your average programmer, and you got to respect that more than anything.
He uses Java, there's only so much stink you can remove from Java code, mostly you just push it around and try to make it as small as possible. Java is still a decent production language for some tasks, but its lack of some basic features and syntactic niceties means you have to hold your nose while coding most of the time.
Can you provide any examples? Was it the tools he was using, notes he was making, or diagrams he was drawing? I haven't seen him program, so I'm curious as to what makes him so much more productive.