If you're talking about skateboarding....
The scene in Japan isn't that big. Basically, skating is allowed only in public parks and, obviously, in private skateparks.
For a list of Japan's biggest skateparks, check this site
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J-Skateboard.com
About skating in public parks... as for Tokyo, I've seen skaters in Ueno koen (mainly in the area in front of the museum), in the park between Tokyo Metropolitan Governement office and Park Hyatt in Shinjuku and in Yoyogi koen, but I'm sure there are a lot more places where j-skateboarders gather.
Skating outside parks (i.e. on the road) isn't illegal, but the cops don't like it and often force skaters to stop their activity and to move to some other place.
More infos:
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Skating in Japan
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J-Skateboard.com (excellent site. in english!)