I agree, back up your data.
If it were me, I'd take the side panel off the case for a while and see if I could catch it clunking. You should be able to narrow it down. As others have said, there isn't much in a computer to clunk. In the average system there are fans and drives. You'll generally have a fan on your processor and maybe one for your power supply. If you have a dedicated graphics card, that might have a fan.
If your hard drive is making much more noise other than clicks and whirrs, it might have a problem. Really bad sounds for a hard drive include screeching or squalling (might mean that the head is comng in contact with the platter, AKA "head crash") or a rythmic, predictable clicking. Like five clicks a little less than a second apart, whirrrrrr, repeat. If your drive sounds like a caffinated squirrel on a telegraph key, that's pretty normal. If it sounds like Stephen Hawking trying to blink for help, that could be bad.