Not much has been written on the non-mention of Japan. The simplest explanation for this is simply that the US and Japan have such a long lasting alliance, and Japan is such an assumed partner of the US, that a mention wasn't necessary. England wasn't mentioned either. (Along with the United Kingdom and Britain)
While Japanese officials' public reaction was calm, there are some reports of shock among the Japanese government at their non-mention.
As concerning as this may seem, it's important to note that Obama hasn't mentioned Japan in past States of the Union. Additionally, Obama's central message was about US competitiveness, especially against rising powers, and as much as 2011 resembles the 80s, Japan as a rising power isn't a hot idea right now.
The bottom line is that language matters. Which countries Obama mentions and how many times clearly indicate where the United States will expend its foreign energy in the coming year. In some cases, like North Korea, it's to counter a military threat. And in others, like India and China, it's to counter an economic threat. Still, from Japan's internal governmental perspective, it can't be good when the President of the United States mentions every country in the neighborhood except Japan. It's kind of like being one of the last chosen for a pick up game of basketball. Your welcome on the team, but you're not worth a high pick. You probably also won't get passed the ball too much.
