I don't know. They both feature UFO-like objects on their retail packaging...
Gigabyte experience: Smartly packaged, solidly packed motherboard, along with a detailed user guide, a large poster with step-by-step installation instructions, and case sticker detailing DIP switch and front panel assignments. Upon installation, technician realizes he's forgotten to set the FSB speed DIP switch, but everything is utterly stable.
MSI experience: After digging motherboard out from under included MSI promotional materials (I think it's supposed to be a calendar), technician finds a manual, written in german. Fortunately, the technician reads german well enough to translate the instructions on the first page: "Slap everything in and pray, kemosabe". The board is utterly jumperless, so the technician does exactly that, encountering several problems that could probably be solved with the included diagnostic LEDs, if the manual made clear how the DLED's green and amber lights matched the black and white used in the (german language) manual. After realizing that by "pray", MSI actually meant "pray to the dark god Nyarlathotep, mother of 1000 goats", the technician makes virgin sacrifices under a gibbous moon on alternating Tuesdays, and replaces the brand name RAM with some cheap generic crap. At last, the motherboard boots.
And immediately crashes, freezing while actually in the BIOS.
After trying a couple different CPUs and dancing the unholy rituals of the snake-god Yig, the technician finally says "screw it" and bumps the CPU voltage a couple notches, letting the system boot long enough to install an operating system...
Which runs fine, unless you install the cursed program "Winzip", which for reasons known only to mad arab prophets and demented playwrights, causes the hard disk attached to the MSI motherboard to start ladder-seeking in a pattern that bears an uncanny resemblance to "My Heart Will Go On".
I'll say there's some differences between the two!