HandBrake's High Profile preset enables 2 poorly-threaded filters (decomb, and more importantly detelecine) by default.
Ah, I didn't realize that. So if the filters in play are poorly-threaded, does that mean hyperthreading is having more of an effect vs. if they were turned off and the main encoding process occupied more of the cycles? I was under the impression that if there were no decombing or detelcining needed, the filters would detect this and turn off. That said, if I find myself in an Apple Store with an i7 machine, I'll turn off the decomb and detelecine and see if it makes any difference.
Edit: Also, DV at 60 fps? Are you sure it's not 480i60 (60 fields per second)? That's likely causing some more time spent in the filters vs. actually encoding in x264.
It's 480p60. The original source was indeed 480i60, but I deinterlaced it beforehand with JES Deinterlacer to make it 60 full frames per second. For the source footage I'm working with (video games with a lot of rapid movement), it makes a big difference in quality.