Stock CPU coolers come free with your CPU but are often too noisy for HTPC use.
Intel’s S- (power saving) and T- (thin chassis) models have slightly quieter cooling fans, but they still are not on par with the best coolers.
I would recommend getting an aftermarket CPU cooler such as Noctua NH-L9A (AMD), NH-L9I (Intel) or Scythe Big Shuriken 2 (AMD or Intel), which are designed to be quiet.
When choosing a CPU cooler, go for the largest cooler possible that will fit in your case.
Normally, larger fans can operate at lower RPMs, which minimize noise while concurrently providing enough airflow for the processor.