I am looking to build a dual GPU (2x Radeon HD 7970) machine on this motherboard; however, I want to run some flavor of Gnu-Linux x64 (likely Xubuntu or Debian). I have read that newer ASUS boards are not friendly to Linux. Does anyone have any personal experience here?
I haven't heard anything about ASUS's newer boards being any less friendly to Linux than any other boards. I got a very newly-introduced ASUS board about a year and a half ago and it worked perfectly out of the box with Gentoo. Some super-high-end ones like the Rampage you listed often have some third-party chips which may be variably supported, but the core chipsets features work.
Looking at the specs, most things should work. There doesn't need to be specific support for the X79 chipset since the chipset functions that need a driver have individual drivers for those functions, not just one "X79 driver." The SATA ports from the Intel chipset work as they are standard AHCI units. Not so sure about the extra ones from the ASMedia one. They could be AHCI compliant as well and would work, but I can't prove that. Ethernet is Intel PCIe and will work. Bluetooth is a standard, will work. Audio should work. USB 3.0 is a standard (XHCI) and will work. The overclocking stuff not done in the BIOS probably won't work as it requires a Windows dashboard program to work. Your Radeon 7970s will work, albeit it takes the very latest Catalyst/fglrx driver to function, and CrossFire doesn't do a whole lot under Linux.