I had popping and crackling in my system which seems to have been caused by USB. I disabled the Root Hub, but left the Controller enabled. That fixed the problem for me. It also allows me to use the USB when necessary by simply re-enabling the Root Hub. If you disable in the BIOS you will have to re-boot anytime you want to use USB, and then reboot again to turn it off.
I assume you are disabling due to some problem. Did disabling the hub not fix your problems? If so, it *may* be that USB is not your problem.
I understand that ACPI might be another source for these type of problems - particularly if you are running Win 2000 or XP. Apparently ACPI causes all PCI cards to share the same IRQ. You might try switching to Standard PC mode if any of this sounds like it applies to your case.