As pointed out by another poster, the scene of the island, supposedly near Macau, where Silva is hiding in Skyfall was filmed at Pinewood Studios in the UK, but it is based on an island in Kyushu Japan called Gunkanjima, and the views of James Bond approaching the island by sailboat in Skyfall show the original island in Japan but with computer graphic enhacements. Here's my post on the actual island: Gunkanjima (Battleship Island)

As for locations in Hong Kong, below is an excerpt from a post of mine about the location of the Bottoms Up Club in Kowloon that appears in The Man with the Golden Gun:
"Back in the mid-90s, I was staying at the Hyatt Hotel on Nathan Road (I'm not sure if it exists anymore) in Kowloon. In the morning I exited the hotel's main entrance on Nathan Road, walked to the right, turned right on the first street I came to and after walking a block or two I crossed the street and while looking to my right I noticed a sign hanging in front of a shop with a very familiar-looking design. I walked toward it to get a closer look and it was a sign for the Bottoms Up Nightclub (on Hangkow Road), a sign that was prominently displayed in the James Bond movie The Man with the Golden Gun. Curious, I descended the stairs to its entrance. It was still too early for it to be open but I thought I might catch an evening show but it turned out to be closed that night, so I wouldn't be able to see it. The movie included a topless bartender scene that was supposedly filmed there, but I'm sure it was filmed in a studio, though the sign and street entrance were the same as in the film, so the exterior was clearly filmed on location." The full post (#43) can be seen at the link below
HK Nostalgia Trip

For James Bond movie locations in Japan, see this thread:
James Bond/Ian Fleming in Japan