I am an American staying in Japan on a short-term tourist visa. I got a tourist visa for China at the Embassy in Tokyo, applying Dec. 21, 2009 and returning to pick up the visa Dec. 22, 2009. (I paid 3000 yen extra for rush service.) Perhaps my experience will help others who have questions.
I took along a copy of my passport (picture page and page with Japanese Landing Permission and Embarkation Card folded out) and a photo from a photo booth (my photo was 35mm x 45mm). I also made a copy of my passport to keep, since they keep your passport while processing the visa application. You can make photos and photocopies at the embassy, but you'll have to pay and wait in line.
I got the visa before I booked a flight or hotel. Nobody at the embassy asked me anything about that. The application asks what's the earliest you plan to go, how long you will stay, and what cities you will visit, but not about flights or hotels.
I paid nothing to submit the application and a total of 18000 yen (cash only) when I picked up my passport with the visa in it. The visa consumes a full page in the passport, but they say two blank visa pages are required.
I guess I was at the embassy a bit more than an hour. There's a bathroom available.
If you arrive at Roppongi metro station, the shortest route is through the West Walk of Roppongi Hills and past the Hyatt.