Excellent episode! It had extremely high production values with no bias from the creators who had an obvious love for both characters.
As for the battle itself, Goku would win. I think something that was a hindrance to Goku for this episode is that his power isn't as clearly defined, so it's difficult to put him against someone who's powers are defined. My only real criticism is that they didn't take into account that Goku's power isn't static, but increases over the course of the series. For example, they used a bit from Snake Way to calculate his max speed, which was awesome, but the problem is that that would end up being his max speed at that point in the series. He'd be moving quite a bit faster later on.
I had actually underestimated Superman coming into this fight. I had always assumed Goku would wipe the floor with him easily. After learning more about his power, I can see that this would be a much closer fight, but I'm still comfortable in saying Goku would win. I think that he was at a disadvantage in this fight because the creators had to give specifics on what his limits were, so they erred on the side of caution. It made for an excellent episode, absolutely, but at the same time a real debate of a battle between these two isn't nearly so cut-and-dry.
So, yeah. Even if I disagree with the outcome, great episode!