A few comments in passing (I have not looked at the neogaf thread):
1. There is Options -> Timing -> Synchronize to refresh rate. Whether or not it behaves how you expect it to / want it to is unknown.
2. The behaviour of "waiting for Vsync" greatly varies and is fully dependent upon the following items, all independently (meaning there are many, MANY combinations to try):
2a. Windows version used -- Windows XP handles Vsync (in DirectX) very differently than Windows Vista and Windows 7.
2b. If the application is running in true full-screen mode or windowed mode. "Using windowed mode but the window is maximised" is not the same thing as full-screen (DirectX handles these very differently).
2c. Video card driver versions and "application profile settings". The latter refers to how most card manufacturers can now let you toggle features or capabilities on a per-executable (per-program) basis, and are 100% independent of whatever options can be selected within that program. There are also often global defaults; some driver versions often default to "Vsync disabled / not allowed" to increase framerate maximums.
2d. Monitor/display profile (.INF) oddities; for example, my Dell 2407FPW out-of-the-box provides only one frequency rate: 60.0Hz. However, on Windows 7, if I update the monitor profile to what Microsoft Update provides, I end up with two choices: 59.9Hz and 60.0Hz (and the default becomes 59.9Hz). Who's to blame for this one? My point is that not everyone who's tinkering about with monitor/display profiles knows what they're doing, and that includes the manufacturer of the product (the actual vendor/engineering group that makes the monitor is more often than not a different division than who makes the .INF file. Toss language barriers into the mix and you're left with nothing but a big mess and an angry consumer).
2e. The software/application itself. Yes, it's true that many applications don't wait for VBlank correctly, or do so in a wonky way. These applications are often written by programmers who are not aware of the aforementioned items/differences. To make matters worse, end-users often report problems with Vsync in such a way (lack of information -- your post is an example, actually! No offence intended!) that results in the programmer "messing around" and causing problems for some while "fixing" it for others.
3. The author of Nestopia, Martin Freij, has disappeared. Many people have Emailed him or attempted to track him down, with no response. He's assumed either extremely busy or dead (not kidding). Martin has also never participated in this forum, to my knowledge. This forum is separate/independent.
