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Across 16 different threaded and single-threaded applications, not counting games, Core i7-3960X is about 12% faster than Core i7-990X.
Price-wise, the processors are pretty comparable, though remember that Intel isn’t bundling a cooler with its Sandy Bridge-E-based CPUs. Also, you’ll need an X79-based motherboard and a quad-channel memory kit.
That’s an expensive list of upgrades for a 12% boost if you already own Core i7-990X. But if you have money burning a hole in your pocket, this flagship most certainly outperforms the old one.