Every 3 seconds is a long period. It's probably not a fan as they are rotating in the hundreds of rpm...unless it's a sticky ball bearing.
Does it sound like an electronic noise? Maybe there is a coil or cap that is acting badly.
Here's a long shot: Maybe there is a cable (like a fan cable) that's near a fan. A blade hits it, it makes the sound as it kicks the cable away for 3 seconds.
Here's a suggestion: get an empty paper towel tube or anything of similar size and use it as a poor man's stethescope to help isolate the sound. Let the PC warm up with the side door open. Then start moving the tube around until you find the source.