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I wanted to update this thread since TrueCrypt 5.1a is out now. They've increased the speed of AES encryption/decryption by 30-140% based on the system, and enabled hibernation on encrypted system drives. I've also been using a fully encrypted system disk since February and haven't really noticed any performance drops.
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"Empirically observed covariation is a necessary but not sufficient condition for causality" - Edward Tufte
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