I noticed a couple of days ago that emerge was running slower than usual and that the rest of my system would come to a crawl while trying to do other things. After looking at gkrellm and dmesg, I find that the kernel only activated one CPU, even though I have a quad core system and the kernel has SMP activated, the correct CPU, and the correct number of max CPUs/cores. I'm going to upgrade my kernel now and hope that this fixes the problem.
Update: After upgrading the kernel (and a few recompiles of the kernel), it looks like the problem was not having ACPI support compiled into the kernel. dmesg did show a message saying there is a bug in the BIOS, that it would be using some kind of default hardware profile, and to contact the hardware vendor on the BIOS bug. A search did show someone else who had this problem that apparently had it go away after compiling ACPI into the kernel, which appears to be the case for me.