I am having a very similar issue, With my gameplay durring everquest 2, My computer freezes after a long time the first time, after my compute has been idle for a while, but after i restart and play eq2, it will most likely freeze after 30 min or so, My sound skips, and makes a clicking noise, but this is the sound alone, When i turn off the speakers the clicking goes away, meaning that the sound isnt coming from hardware. My cooling is quite nice, my case temp is usually between 29-32 degrees, and my processor, is usually 43-45 degrees, Usually between 45-47 when playing everquest2.

computer specs
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3.0GHZ Pentium 4 with HT
74gb WD Raptor 10,000rpm hd
soyo dragon 2 black edition motherboard
1gb Nitro highspeed ram
256 xtasy ati agp video card
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I have been having this problem for months now, since about november, but untill now, i am fed up with it happening. But just to let thief know, that he isnt the only one having this problem.