Microsecond resolution timestamps on Windows
I believe this is still useful: System Internals: Guidelines For Providing Multimedia Timer Support.
It does a good job of explaining the various timers available and their limitations. It might be that your archenemy will not so much be resolution, but latency.
QueryPerformanceCounter will not always run at CPU speed. In fact, it might try to avoid RDTSC, especially on multi-processor(/multi-core) systems: it will use the HPET on Windows Vista and later if it is available or the ACPI/PM timer. On my system (Windows 7 x64, dual core AMD) the timer runs at 14.31818 MHz.
The same is true for earlier systems:
By default, Windows Server 2003 Service Pack 2 (SP2) uses the PM timer for all multiprocessor APIC or ACPI HALs, unless the check process to determine whether the BIOS supports the APIC or ACPI HALs fails."
The problem is, when the check fails. This simply means that your computer/BIOS is broken in a way. Then you might either fix your BIOS (recommended), or at least switch to using the ACPI timer (/usepmtimer) for the time being.
It is easy from C# - without P/Invoke - to check for high-resolution timer support with Stopwatch.IsHighResolution and then peek at Stopwatch.Frequency. It will make the necessary QueryPerformanceCounter call internally.
Also consider that if the timers are broken, the whole system will go havoc and in general, behave strangely, reporting negative elapsed times, slowing down, etc. - not just your application.
This means that you can actually rely on QueryPerformanceCounter.
... and contrary to popular belief, QueryPerformanceFrequency() "cannot change while the system is running".
Edit: As the documentation on QueryPerformanceCounter() states, "it should not matter which processor is called" - and in fact the whole hacking around with thread affinity is only needed if the APIC/ACPI detection fails and the system resorts to using the TSC. It is a resort that should not happen. If it happens on older systems, there is likely a BIOS update/driver fix from the manufacturer. If there is none, the /usepmtimer boot switch is still there. If that fails as well, because the system does not have a proper timer apart from the Pentium TSC, you might in fact consider messing with thread affinity - even then, the sample provided by others in the "Community Content" area of the page is misleading as it has a non-negligible overhead due to setting thread affinity on every start/stop call - that introduces considerable latency and likely diminishes the benefits of using a high resolution timer in the first place.
Game Timing and Multicore Processors is a recommendation on how to use them properly. Please consider that it is now five years old, and at that time fewer systems were fully ACPI compliant/supported - that is why while bashing it, the article goes into so much detail about TSC and how to work around its limitations by keeping an affine thread.
I believe it is a fairly hard task nowadays to find a common PC with zero ACPI support and no usable PM timer. The most common case is probably BIOS settings, when ACPI support is incorrectly set (sometimes sadly by factory defaults).
Anecdotes tell that eight years ago, the situation was different in rare cases. (Makes a fun read, developers working around design "shortcomings" and bashing chip designers. To be fair, it might be the same way vice versa. :-)
QueryPerformanceCounter / QueryPerformanceFrequency, processor speed resolution
Just be careful with multi-threaded. Each core on a processor can have its own counter.
Some more information is in Obtaining Accurate Timestamps under Windows XP.
If you do end up having to resort to this method:
When I was trying to manually write data to a serial port (for an infrared transmitter) I found that setting the process and thread priority to maximum (real time) greatly improved its reliability (as in no errors), this is something that had to have a resolution of around 40 kHz if I remember too, so it should remain accurate enough for millisecond resolution.
Windows is not a real-time OS.
Processes on a multitasking OS will need to yield its time to another thread/process. This gives some overhead for timing.
Every function call will have overhead thus giving a little delay when returning the request.
Furthermore, the calling system call will need your process to switch from user space mode to kernel space mode, which has relatively high latency. You can overcome this by running the entire process in kernel mode (such as device driver code).
Some OSes, like Linux or BSD, are better, but they still can not maintain accurate timing resolution to sub-microsecond (for example, the accuracy of nanosleep() on Linux is about 1 ms, not less than 1 ms), except you patch the kernel to some specific scheduler that give your application benefits.
So I think, it's better to adapt your application to follow those issues, such as by recalibrating your timing routine often, which is what your links provide. AFAIK, the highest timer resolution for Windows is still GetPerformanceCounter/Frequency() regardless of its accuracy. You can get better accuracy by running you timer pooling routine inside a separate thread, and set that thread affinity to one core processor, and set the thread priority the highest you can get.