besides speedfan which i personally perfer over the manufacturer tools (which testing has proven to be often inaccurate) there is the option of hardware thermal monitoring. some choices can be seen here. As an overclocker I personally prefer hardware based thermal monitoring. There is also the option of using some of the customizable LCD controls that support thermal sensors but that is a little off topic.

on a side note my personal mobo makes funny sounds at strange times as well when performing some tasks. its just a strange thing that happens (im not sure why).