The motherboard is possibly the most important part of the computer. It manages all transactions of data between CPU and the peripherals. It houses the CPU and its second level cache, the chipset, the BIOS, main memory, I/O chips, ports for keyboard, serial I/O, parallel I/O, disks and plug-in cards.
The first decision you have to make before buying a motherboard is nowadays which CPU and then which chipset you're gonna use. So probably it's best to first refer to the Chipset Guide. The next thing is to choose the manufacturer. There's no doubt about it - you really should go for a brand motherboard, preferably a brand that's present on the web, because that is by far the best way to get the latest Flash BIOS update, drivers and information about the board you might require.
New Testing Policy
I've started motherboard testing and publishing on the Internet roughly two years ago now and I think it's about time for taking this testing into the next phase. Whilst in the past I focussed on the performance aspect of motherboards, now I think other topics are at least as important as well.
The difference in motherboard performance between the 'slowest' and the 'fastest' boards does nowadays hardly exceed the 3% range anymore, so that recommendations purely based on performance get pretty close to bean counting. What counts much more to the users and system integrators as well as the large OEMs is the usebility of a motherboard.
In the past I came across a lot of problems myself, as well as I received a lot of mail from confused readers. A typical example is the pretty common difficulty of getting several PCI or ISA cards to work in a motherboard, something that is getting even worse when there are already more than two of these cards running in the system. E.g. Abit's LX6 board, which became so famous for overclocking, was a nightmare when you wanted to use more than only an AGP graphics card in the system. Problems started latest when one decided to plug in SCSI and/or network cards as well.