Have you tried the rolled up paper method of locating the source. Tricky for such an intermittent problem, but it can be very effective. Roll a sheet of A4 paper into a long tube. One end against your ear and use the other end to locate the noise source.
Possible noise sources - hard drive, case fan, graphics fan, CPU fan, chipset fan, PSU fan, wire touching any of the fans. Does your computer have any relays? Uncommon but possible. Could the noise be purely mechanical due to expansion of a hot component? I've never come across this causing a noise in a computer but it would cause a very intermittent noise.