perhaps a fan bearing is acting up, I had one do that for a while, make a funny low pitch sound then stop then start up again, then stop... drove me nuts for a week or two and was about to go pick up a new one before it froze completely but it just stopped making the noise, that was months ago and it's been quiet ever since...
do you have a modem in there? they have those little speakers on em maybe it's malfunctioning, stick a piece of black tape over it, or snip the wires, that'll shut it up.
it may also just be some vibration humming along on some loose board, so you might check for some loose screws in yer noggin
or just grab a bottle of scotch and hum along.
hehe hope you find the noise man