Its going to vary depending on chipsets a bit too.
For instance, the 790I ultra sli chipset is E-vgas top board - but like all 790I ultra boards it has display corruption problems while playing dvds and the like that Nvidia has failed to resolve - this is pretty much a problem widespread over many SLI chipsets.
The fact is, you can't really fault E-vga for that, or XFX or any other SLI board maker - thats just how the chip is. Anyways, this can vary across any board and any company. You have to research the technology a bit too and make an educated decision if you are investing in something you intend to keep for quite a while.
oogle reviews and whatnot, pay more attention to reviews done by enthusiast sites as they tend to be more critical. Like gators1223 said, gigabyte/msi/asus/evga all make exceptional motherboards with their various perks - but just make sure the technology suits your needs and if there are any bugs in the tech, that they aren't going to regularly interfere with your goals for the PC and you'll be happy.