It's been years since the idea of "trusted computing" was first mooted -- a hardware layer for PCs that can verify that your OS matches the version the vendor created. At the time, TC advocates proposed that this would be most useful for thwarting malicious software, like rootkits, that compromise user privacy and security.
But from the start, civil liberties people have worried that there was a danger that TC could be used to lock hardware to specific vendors' operating systems, and prevent you from, for example, tossing out Windows and installing GNU/Linux on your PC.
The latest iteration of Trusted Computing is called "UEFI," and boards are starting to ship with UEFI hardware that can prevent the machine from loading altered operating systems. This would be a great boon to users -- if the PC vendors supplied the keys necessary to unlock the UEFI module and load your own OS. That way, UEFI could verify the integrity of any OS you chose to run.
But PC vendors -- either out of laziness or some more sinister motive -- may choose not to release those keys, and as a result, PC hardware could enter the market that is technically capable of running GNU/Linux, but which will not allow you to run any OS other than Windows.
What's more, UEFI may fall into the category of "effective access control for a copyrighted work," which means that breaking it would be illegal under the DMCA -- in other words, it could be illegal to choose to run any OS other than the one that the hardware vendor supplied.
Secure boot is optional, but there is likely to be a fair amount of pressure applied by proprietary OS makers to enable it. One could imagine that those vendors might also provide a way to turn off secure boot (from a BIOS-like menu for example), but that is something that might be exploited by rootkits and other malware, so there may well be resistance to allowing that kind of option. Protecting users from rootkits and the like is certainly useful, but there is a competitive advantage as well. Hardware vendors can ensure that only the code they approve can run on the hardware, and proprietary OS vendors will be largely unaffected because their keys will be in the signature database. One would hope that the protection against malware is the primary motivation, but the ability to lock out free OSes is likely seen as a plus.
It is Linux and other free systems that could suffer most from secure boot implementations. While it would be possible for various distributions to get their keys added, that wouldn't help anyone who wanted to run a tweaked version of the "approved" bootloader or kernel. Distributors would not be able to release their private keys to allow folks to sign their own binaries either. Each key is just as valid as any other, so malware authors would just pick up those keys to sign their wares. Exposed keys would also find their way onto the forbidden list rather quickly one suspects.