1. ShinjukuShinjuku is a large business, entertainment and shopping district centered around JR Shinjuku Station. It's the busiest train station in the world (Guinness World Record) handling 3.64 million passengers a day.
The west side of the station is a business district that includes the massive Tokyo City Hall building. The south side of the station is primarily a shopping area. To the east of the station lies Kabukicho (Asia's biggest red-light district).
All 3 sides of the station are unbelievably busy 7 days a week (the west side is somewhat quiet on weekends). The station itself isn't particularly large given the high passenger throughput. It's almost certainly the most crowded building in the world.
2. IkebukuroIkebukuro station is the world's second busiest station (2.71 million passengers a day). Like Shinjuku, Ikebukuro is a crowded shopping, dining and entertainment district.
3. ShibuyaShibuya is a large shopping and entertainment district best known for it's busy pedestrian crossing. Shibuya crossing is the busiest pedestrian crossing in the world. Estimates are that almost 1 million people cross the street here each day (2.18 million people use Shibuya station daily).
4. YokohamaYokohama isn't in Tokyo. It's part of Kanagawa prefecture. However, it's often considered part of the greater Tokyo area.
Yokohama station handles 2.09 million passengers a day (almost as many as Shibuya station). The Yokohama area is a major business, residential, shopping and entertainment district.
5. Tokyo Station Area (Marunouchi & Yaesu)Tokyo station handles over a million passengers a day. It's Tokyo's intercity rail hub connecting Tokyo with the rest of Japan by Shinkansen (bullet train). More trains pass through Tokyo station each day than any other station in Japan.
Tokyo station also serves two of the cities largest business districts: Marunouchi and Yaesu.
6. ShinagawaShinagawa station and Tokyo station are Tokyo's two main Shinkansen (bullet train) hubs*. Shinagawa station handles close to a million passengers a day. Shinagawa is a busy business, dining and nightlife area.
7. ShinbashiShinbashi is one of Tokyo's largest business districts. It's unbelievably crowded on weekdays. It's morning rush is a sea of black suits. Salary men relax after work in the area's many izakaya and restaurants. Shinbashi is almost completely deserted on weekends.
Honorable Mention: NakanoNakano is the most densely populated residential neighborhood in Tokyo. The streets of Nakano aren't particularly crowded but there are almost 20,000 people per km2 living there. Despite the crowding Nakano is a highly rated residential neighborhood known for its laid-back atmosphere.