For Singapore, you can also try the bar on top of Raffles Place, 1Altitude. You probably can't get a tripod in there, but it has some great views. If you want the typical Merlion and skyline from the Marina view, take a taxi to Esplande. This is very nice around 7pm, right at sunset. (Since Singapore is just north of the equator, sunrise and sunset times are pretty static at about ~7:15 each the whole year)
If you have a clear day and a really long lens, go out to Bedok Jetty. It's maybe 15 minutes by cab from CBD. You can get a very wide angle of the East Coast and the skyline. (more of the skyline the longer your lens is). It's also an excellent spot to capture nice storm clouds rolling in.
For Tokyo, two places I can recommend that I just got back from last week, almost the same view in each. Park Hyatt Tokyo (hotel from Lost in Translation) and Tokyo Opera City. These are the tallest and furthest west buildings in Shinjuku skyscraper city. They have some nice unique views of their own. My favorite was of Yoyogi Park / Meiji Shrine with Tokyo Tower/Roppongi in the back. For Park Hyatt, you can get into the lounge on 42 pretty easily. For Tokyo Opera City, there are a bunch of relatively inexpensive (~1500y for lunch) restaurants on 54th floor that have great views. Tripods may be a problem in both though.
DrMarkF on page 4 had some of the best advice for Hong Kong. Go to the peak, but walk along the trail west for excellent shots. Another great option on a clear day is some of the views from Lion Rock. The Promenade in TST is nice, but thats the shot everyone takes. If you want to see some amazing shots of HK and get idea for places to shoot from, you can check a friend's facebook page: facebook.com/HongKongHDR
In Chicago, Alder Planetarum/Museum campus is indeed tops. John Hancock is nice, but you have to deal with tinted glass.
In San Francisco, there are a series of building rooftops designated "public gardens". These are excellent spots. Many buildings keep them very discreet though; I believe they were only installed as a way to get the permit from the city or some kind of tax break. If you Google a bit, you can find articles on them. The other two good spots are from Treasure/Yerba Buena Island (take the Bay Bridge east to Oakland, it is the only exit from the bridge in the middle, on the left. ) Also, Twin Peaks, which is the "Noe Valley radio tower" mentioned earlier.