The MSI X79A-GD65 (8D) comes with a few advantages and several disadvantages compared to its main competitor, the Gigabyte X79-UD3.
On the positive side, it has eight memory sockets, two FireWire ports, a POST diagnostics display, better components in the voltage regulator circuit, and the handy “OC Genie” button.
However, the list of drawbacks is quite extensive. This motherboard has five PCI Express x16 slots, but you can only install three dual-slot video cards (the competing model from Gigabyte accepts four). These slots are configured as x16/x16/x8/x1/x1, while on the Gigabyte motherboard the four available slots are configured as x16/x16/x8 when using up to three video cards or as x16/x8/x8/x8 when four video cards are present. What is the point of having five PCI Express x16 slots if you can only use three of them?
For some reason we can’t understand, MSI used a mainstream audio codec (Realtek ALC892) on a motherboard targeted to high-end users. If you are going to work converting analog audio sources (e.g., LP records, VHS tapes, cassette tapes, etc.) to the digital format, you will need to pick a different motherboard, as the input signal-to-noise ratio of this codec is 90 dB, which is too low for this application. (Translation: You will inject a lot of noise into your work.)
This motherboard has only two additional SATA-600 ports, and the manufacturer should have used a different color on them. The Gigabyte X79-UD3 has four additional SATA-600 ports and two independent eSATA-600 ports, which are not available on the MSI X79A-GD65 (8D). The MSI model comes with an adapter to convert two SATA ports into eSATA, though.
On the overclocking side, even though the MSI X79A-GD65 (8D) has voltage monitoring points and the “OC Genie” button, the Gigabyte X79-UD3’s setup has far more overclocking options.
And, finally, we have pricing: the MSI X79A-GD65 (8D) has fewer features yet is more expensive than the Gigabyte X79-UD3. Because of all the reasons described here, we prefer the Gigabyte X79-UD3 over the MSI X79A-GD65 (8D).