So I'll try to explain the problem a little more. I like to sleep with my computer still running, normally the build is really damn quiet. However sometimes after its been in standby for awhile, the fans will sky rocket and it will sound like a jet for maybe a minute or so and return to normal.
Any ideas of what I can do to isolate the problem, or maybe someone has a solution for it.
My guess would be the CPU fan is the one that got loud. Most BIOS have an option that automatically controls CPU fan speed, based on the CPU temperature. AMD CPUs are controlled by Cool 'n Quiet, while Intel CPUs are controlled by Speedstep.
These technologies allow the CPU fan to speed up to keep the CPU cool, but also allow the fan to slow down to save power, when the CPU isn't under heavy load. If you have a system that you built yourself (as opposed to an off-the-shelf style), you should be able to disable Speedstep and C 'n Q, respectively.