A motherboard's chipset typically looks like a PCI-E device to the BIOS. It also can control the appearance of other hardware to the rest of the system and would be most likely to be involved in this function.
The chipset's PCI-E device likely has registers that enable or disable other hardware in the system, as well as "lock bit" registers that say "don't accept any more changes until next reset." The BIOS reads the NVRAM and configures the chipset accordingly, then locks it.
The ability to disable virtualization support, as well as locking this change until reboot, is built-in to the CPU itself, changeable via one of the CPU's MSRs. Some other capability may also be controlled by this mechanism. Again, the BIOS would typically program the MSRs in the desired fashion before handing control to a bootloader.
It's also possible that reads and writes to certain I/O ports, memory addresses, I2C or SMBus addresses can also control the appearance of hardware. Most of this stuff would fall under ACPI.
Would depend on the type of motherboard and BIOS (Basic Input and Output System) being used. Most likely, the BIOS just doesn't tell the system about the devices, so power could still be put through (as a way to charge electronic devices, for instance). – Doktoro Reichard – 2013-10-08T20:43:34.490
Also, what controllers? – Austin T French – 2013-10-08T20:46:47.233
For example the on-board NIC, when I go into the BIOS and disable it and then go into Device Manager, the controller isn't there. I presumed the BIOS cuts power off to the controller. Thanks – RJSmith92 – 2013-10-08T20:50:25.423
@DoktoroReichard That used to be it, except most modern OS's do their own hardware detection/abstraction instead of depending on the BIOS (matters more now that BIOS is becoming Legacy to UEFI). – Ƭᴇcʜιᴇ007 – 2013-10-08T20:52:33.553
I thought it was that @techie007. The OS ignores the BIOS abstraction layer an interacts with the hardware directly. – RJSmith92 – 2013-10-08T20:54:41.047