On a Quad-Core add this to the advanced parameters (HandBrake):

Code:

:threads=3 or this
Code:

:threads=2 on a Dual-Core machine. HandBrake (HB) uses a lot of SSE2/SSE4 instructions, which saturate the memory I/O system (even on SB-machines), so that virtual cores (HT) are not able to improve the performance of the x264 encoder in HB. That means, you should use
Code:

:threads=NumberOfPhysicalCPUCores for maximum performance and

Code:

:threads=(NumberOfPhysicalCPUCores / 2) + 1 for lower temperatures (RAM & CPU semiconductors). +1 is for the I/O thread. Some other tricks: Use the "renice" command (Terminal) to give HB a lower priority:
Code:

sudo renice 19 PID "PID" is the process id, which you can find via Activity Monitor or via the
Code:

top command in a Terminal window. You can reduce the CPU usage of some apps via the Terminal, if you know you do not need them (a web browser for example):
Code:

kill -SIGSTOP PID reduces the CPU usage of the process with the process id "PID" to zero.
Code:

kill -SIGCONT PID resumes the process with the process id "PID"