1 & 2) Tokyo Disneyland and Tokyo Disney Sea
Probably the most popular theme parks in Japan are Tokyo Disneyland and Tokyo Disney Sea. Tokyo Disneyland is oriented more towards children but Disney Sea is targeted at the adults and has a nautical theme with the rides being faster and scarier.
The main areas at Disney Sea are a Mediterranean Harbor, Mysterious Island, Mermaid Lagoon, Arabian Coast, Lost River Delta, Port Discovery, and American Waterfront. There are also hotels to stay in and alcohol is served inside the park. For those with young children in tow, there are several attractions for them and a babysitting service.
If you want to get wet, a great way to kill some time is Laqua, which is located centrally in Suidobashi. They have a spa, an amusement park and a restaurant and shopping area. The spa is a five floor complex with a variety of spas, sauna, bubble massages and a dining and relaxation area.
4) Yomiuri Land
Yomiuri Land is a massive sprawling amusement park in the west outskirts of Tokyo.
Hanayashiki, Japan's oldest amusement park is in the back of Asakusa near the ROX.
6) FujiQ Highland
A great theme park for thrill seekers is FujiQ Highland, which has Mount Fuji in the background. But, the lines can be up to 90 minutes and if you are going there just for the rides and not the scenery you might be better off visiting one of the local amusement parks like Toshimaen or Yomiuri Land.
7) Universal Studios
Universal Studios, located in Osaka is almost an exact copy of the Florida Universal Studios.
Toshimaen is a very popular amusement park located in Nerima-ward. In summer there is a huge pool complex with water slides which is extremely popular with families and young adults.
9) Sanrio Puroland
If you have little kids, then Sanrio Puroland (the home of Hello Kitty) is a good option. Some nice rides there include Sanrio Character Boat Ride and a few more tamer rides the kids will love.
10) Yokohama Cosmoworld
Yokohama Cosmoworld is a really nice little amusement park by the sea in the port town of Yokohama.