For Osaka, you'll want to hit up two skyscrapers above all others, both with great public observation floors at their tops:
Cosmo Tower (http://www.wtc-cosmotower.com/
, Japanese only): 2nd tallest tower in Japan and standing alone out on the bay, this gives you unobstructed views of the entire Osaka shoreline metro, including Kobe.
Umeda Sky Building (http://www.kuchu-teien.com/english/index.html
, English): A really funky tower with a large open air observatory on the roof, offers up-close views of Umeda, the main CBD / Shinjuku of Osaka.