pfft, I've had the i7 930 at 4.4Ghz on air cooling before. 4.2Ghz ued to be my main oc until I decided to go to 4Ghz instead because it was my sweet spot.
I turned off hyper threading and the problem persists.
OK, it's been a while but I think I finally figured out what is causing the stuttering. I ran dolphin alongside GPU-Z and I noticed sometimes my graphics card tries to switch to idle mode and the Bus interface switches to PCI-E x1 v 1.1 from PCI-E x16 v.3.0 for a second.
Does this mean that Dolphin isn't stressing my graphics card enough so it tries to switch to low power mode, then it quickly figures out that it can't run it in low power mode, switches back, and that's what causes the stutter? How do I get my power card to stop trying to switch to idle mode?
You could try just stressing your GPU more and see if that resolves anything; increase IR to 4x and enable MSAA.
I use MSI Afterburner with the OSD monitor ("rivatunerstatisticsmonitor") to keep an eye on temps and CPU/GPU usage, you could give that a try:
http://event.msi.com/vga/afterburner/download.htm. That way you can determine what exactly happens during the emulation.
You can try also forcing High Performance settings in nVidia Control Panel