I was there for a few days last summer, but was at the end of a long trip traveling around China so was a bit wrecked and didn't do much. Just wandered about the Imperial Gardens, took in Shinjuku, Shibuya, Roppongi. I was staying in Akasaka, in one of the capsule hotels.
It's an unbelievably clean place. That's the first thing I noticed about it, especially after coming from Hong Kong/China. I made sure to go for a sushi set menu, was class but can't remember the name of the place. It's a small chain, they have a few all around Tokyo; I'll try to find that one out.