The latter is probably one of the reasons why being a patent attorney might be quite a boring job - checking the state of the art, zzzzzzz (edit: woops, sorry JamieG).
Thankfully, I'm not a patent attorney (which normally requires a 'hard' science background). I work more on the commercial side of IP law, but I know enough about patent law that I felt a need to comment.
You're correct on the law here.
That was my point, Apple can apply to patent things that it did not invent or that are not novel or inventive in a legal sense. Patent examiners can and do make mistakes and allow things to be patented that they should not be allowed to patent.
To the extent that most of these functions are present in a BIOS, then this is a system. However, if Apple add a new element and improve on this system (such as hard drive power management or spinning down, or the microphone monitoring mentioned in one of the patents), it could be an inventive step sufficient for patent protection to combine an existing system with new elements, provided that it is not obvious to a person who works in the same area and is not disclosed by the prior art in the same area.
I agree, it is entirely possible that Apple could be awarded these patents if the examiner is not made aware of the various BIOS functions and items mentioned in this thread. However, I don't know whether as part of the USPTO's patent examination system examiners accept letters from third parties - you could always try I suppose.
While the patent process can be expensive (particularly if you want your patent to be granted in the various countries around the world), it can be worth the $$$. I don't know if Canada has a similar system, but here in Australia there is something called an innovation patent, which has a lower threshold for patentability but the period of exclusivity is also lower.
It could have been worth it...