Most often its the fan which make such noise . You should disconnect your fan and see if the noise remain or not . Most often the fan is configured to automatically operate according to processor heat level , so when you use the pc for a long time the processor heats up and pc slow down a little bit and programs may start hanging which in turn take more processing power which signals fan to accelerate which in turn make noise . If fan is not the problem then I guess its hard drive. You should also check for viruses ( there are viruses which start chain processes and make processor heat up )
You can check your Hard Drive's smart status using some programs - HDTune, SpeedFan. The Smart status shows, if the drive is going to fail soon. It might also be the hard drive causing vibrations to the whole PC case, because of improper seating.