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I had a problem somewhat like this a month or so back, although only in a specialized case. Whenever I'd run a somewhat intensive 3D game (Half-Life 2, The Sims 2, even Civilization), the computer would lock up after a few minutes. After tearing my hair out trying all sorts of software solutions, I finally cracked open the case and took a look inside. Turned out the fan on my video card had bit the dust (heh), and the card was overheating and crapping out. Bought a new fan for 15 bucks, installed it, and no more problems.
Don't know if this applies here, as your problem seems more general, but I thought I'd throw it out there. It does definitely sound hardware related though.
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