For the storage tests, we ran our Secondary SSD, a Patriot Pyro SE 60GB through three separate benchmarks, AS SSD, ATTO, and CrystalDiskMark. For the USB tests, CrystalDiskMark was used to measure the transfer speed of our Seagate GoFlex Desktop 2.0TB USB 3.0 hard drive.
One thing is quickly apparent, the Marvell SATA controllers which add an additional four 6GB/s SATA ports do not perform nearly as well as those on the PCH, yielding read performance about halfway in between the 6GB/s and 3GB/s connections. The write speeds of the Marvell controller was also roughly equivalent to that of the 3GB/s SATA ports. Overall, across all of the benchmarks, the ASUS P9X79 and the Gigabyte-X79-UD3 trade blows in SATA performance, as the X79-UD3 is slightly better than the P9X79 in 6GB/s tests, while the P9X79 edges Gigabyte's counterpart in the 3GB/s tests. The Marvell controller on the P9X79 Deluxe is also more geared towards better read speeds, and the write speeds lag.
We see a definitive advantage in favor of the Gigabyte X79-UD3 in the USB 2.0 tests. The USB 3.0 tests were pleasing, with triple the speed being seen over USB 2.0. The USB 3.0 performance on the P9X79 slightly edges out the X79-UD3, but not by a significant amount, and are essentially the same. Both of these USB 3.0 tests are based upon their respective "boosted" performance.