I was under the impression that QueryPerformanceCounter was actually accessing the counter that feeds the HPET (High Performance Event Timer)---the difference of course being that HPET is a timer which send an interrupt when the counter value matches the desired interval whereas to make a timer "out of" QueryPerformanceCounter you have to write your own loop in software.
The only reason I had assumed the hardware behind the two was the same is because somewhere I had read that QueryPerformanceCounter was accessing a counter on the chipset.
http://www.gamedev.net/reference/programming/features/timing/ claims that QueryPerformanceCounter use chipset timers which apparently have a specified clock rate. However, I can verify that QueryPerformanceFrequency returns wildly different numbers on different machines, and in fact, the number can change slightly from boot to boot.
The numbers returned can sometimes be totally ridiculous---implying ticks in the nanosecond range. Of course when put together it all works; that is, writing timer software using QueryPerformanceCounter/QueryPerformanceFrequency allows you to get proper timing and latency is pretty low.
A software timer using these functions can be pretty good. For example, with an interval of 1 millisecond, over 30 seconds it's easy to nearly 100% of ticks to fall within 10% of the intended interval. With an interval of 100 microseconds, you still get a high success rate (99.7%) but the worst ticks can be way off (200 microseconds).
I'm wondering if the clock behind the HPET is the same. Supposedly HPET should still increase accuracy since it is a hardware timer, but as of yet I don't know how to access it in Windows.