There a few things that software could potentially do to destroy your hardware, but they are really just special cases. A one time BIOS change will not hurt your system, but if you repeatedly change voltages to unsafe levels many times over, eventually you will just wear your processor out hundreds of times faster than it otherwise would.

Also, if you don't have good heat venting for your system, or if you say left it in a black bag in a black car in the middle of summer and there was a 100% CPU utilization process running then you *might* find a melted CPU, depending on what safeguards are in place (you could remove these in BIOS).

In general though, there is absolutely NOTHING that software can do by itself to harm your hardware. There are certain pieces of software, though, that if you delete or corrupt will force you to use tools that aren't easily or cheaply available on the market to recover your device. These pieces of software are generally the boot sectors of your system and especially on embedded systems, they may be impossible to recover without special cables or interfacing hardware and opening up the devices innards.