I found this article on Gentoo Forums:
The last note is interesting; problems similar to mine seem to be fixed after changing the time source to tsc. Looking through my logs, I found that my time source changed from pmtmr to tsc on Sept. 20. This corresponds to a kernel update.
I tried changing my time source back by passing the "clock=pmtmr" parameter to the kernel, but that time source is no longer compiled it. It did, however, fall back to pit.
This somewhat agrees with my memory of the problem starting around the time I installed the beta nVidia driver, about a month earlier (Aug. 25).
I'm not going to jinx myself and say that the problem has been resolved, but it's looking good so far.