1) New York Grill in Tokyo - which I'm sure has already been mentioned. Was there in February. Dinner just okay, but great for a drinks and live jazz (now nightly).
2) 20 Up in Hamburg - Top floor of the Empire Riverside Hotel. Amazing panoramic views of the city. Hip crowd.
3) Tower Club at Lebua, Bangkok - which has also been probably mentioned already.
4) Tavola 36 in Osaka - Atop the Swisshotel Nankai. It's an Italian restaurant by night, but it's also used for complimentary breakfasts in the daytime. Not sure this qualifies as a 'skyscraper', though.
5) There's a cafe at the observation deck of one of Tokyo's Metropolitan Government Buildings. Forget which tower has it; maybe both do.
6) Columbia Tower in Seattle - I frequent the Starbucks on the 40th floor. It not only has excellent views, but the layout of the space is nicer than most other Starbucks.