Recently I've been poking around looking at some Time Stamp Counter (TSC) anomalies when coming out of suspend. So what is the TSC? It's a 64 bit high resolution tick counter found on X86 processors (since Pentiums) and can be read using the rdtsc instruction.
It is intended to be a fast method of getting a high resolution timer. However it is known to problematic on multi-core and hyperthreaded CPUs - one needs to be locked to one CPU to get reliable results since the TSC may be different on each CPU. It is also known to reset when coming out of resume which means time can look like it goes backwards in a huge jump.
If the CPU speed is changed then the TSC rate can change too. If you have a more recent Intel CPU where the constant_tsc flag is set (see /proc/cpuinfo) then the TSC will run at a constant rate no matter the CPU speed - but this means that benchmarking with the constant TSC may make programs look like they use more CPU cycles than in reality!
Anyhow, getting the 64 bit TSC value is a simple case of using the rdtsc instruction. I've got some example code to do this here with the necessary inlined assembler magic to handle this correctly for 32 and 64 bit builds.