See Handbrake CPU usage...
What's wrong with my activity monitor?
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Which Mac do you have? – duci9y Jun 23 '13 at 09:55
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Nothing is wrong with your Activity Monitor. 100% is the throughput on one core of a CPU.
Newer Macs (all since 2007?) have CPUs that have more than one core and or also hyper threading. Handbrake can make use of these cores and excite in parallel on more than one core.
mmmmmm
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so a quad-core can arrive to 400%, and with hyperthreading it should theoretically arrive to 800%? – doplumi Jun 23 '13 at 11:34
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SOrt of - hyper threading is not as good as increasing the cores so will depend on what is running – mmmmmm Jun 23 '13 at 13:28