This list is not comprehensive, but here are some of the largest Deck Level developments in Japan:
Senri-Chuo shopping center in Osaka (on airport monorail line): huge deck level. Surrounding park areas are connected by pedestrian bridges, creating near total grade separation of vehicles and pedestrians. Very much like Tama Center. See also: http://senri50.com/c4489.html
Tama Center: Wide deck level stretching 1100′ NW from Keio Tama Center to Parthenon Tama, and 3400′ EW. Similar to Senri-Chuo in Osaka.
JR Osaki (on Yamanote): deck level extends ~2/3 mile from north to south.
Tachikawa Station (west of Tokyo): deck level runs 3,000′ north to south.
Machida: deck and skyways extend ~2800′ from malls by Machida Station down to Machida Terminal Plaza to SE.
Takeshiba Station (south side of Hamarikyu Park): 1,300′ NS, connects two large hotels.
Tsukuba Station: deck level in front of Okura Frontier Hotel (in Ibaraki).
JR Kawagoe (1 hour NW of Shinjuku): medium deck level with some long bridges. Bricked street from north end runs 1/2 mile all the way to Honkawagoe.
Big Site area in East Odaiba. Pallette Town and across the park, in West Odaiba.
Ikebukuro & Shibuya: currently undergoing deck level expansion. http://www.skyscrapercity.com/showthread.php?t=1605205&page=5
Akihabara: skywalk to and around Akiba-ichi biru (mostly escalator access).
Hamamatsucho: glass shaded deck extends to north & south, and new extension reaches west to the closest subway station.
Phrom Phong (Bangkok): EmQuartier and other buildings connected with broad deck. See: http://thinkofliving.com/2015/03/28/emquartier-opening/
Chitlom-Ratchaprasong-Siam-National Stadium Stations: Deck below SkyTrain (above freeway), connects four stations and many major shopping mall/skyscrapers. Over 1 mile east-west. See: https://bangkokjam.wordpress.com/2011/02/23/bangkok-super-skywalk-system/
Diagram of future plan for Shibuya: