The name serves it well. Just like a mother in a household, the motherboard, or mainboard, is the most important piece when building a computer. If you're looking to build a computer you will love, take the most time on picking out this component.
You could save by spending less money on anything else but nothing will effect system stability or performance more than the mainboard.
Everything on your computer plugs into the mainboard in one way or another, knowing them is important so you when you buy your mainboard, you don't buy more components than it can handle.
When looking at any component, it will tell you which connector it needs. Occasionally the interface is hidden in the part number.
PCI - typically the white connector on the board, most often used for connecting components like sound cards, or network cards.
PCIe or PCI Express - common connector for video cards, sometimes used for sounds cards, it is a faster PCI, the two connectors are not interchangeable.
EIDE or IDE - This is a drive connection, either for hard drives blu-ray, or dvd roms, currently just used for the dvd and blu ray roms. You can connect two drives for every connector on the motherboard. The one at the end of the cable is called the master, the one in the middle is called the slave.
SATA or Serial ATA - This is the faster new interface for hard drives, it replaces IDE.
DDR - Often called by many different names DDR2, DDR3, checking the MHz number as well as the DDR number will let you know which RAM it supports.
USB - These days just about anything, from mice to external hard drives connect to these. As long as you have one, you can even buy splitters to get more connections.
Firewire - High end components like fast external hard drives, recording quality external sound cards use these. If you need to transfer large amounts of data outside the computer case this is how to do it.
LAN or Ethernet - Will connect you to a computer network, 10/100 was common for a long time. The current standard is 10/100/1000 or gigabit.
Parallel Port - I've only seen this used to connect printers or home made electronics. Most printers now use USB or even wireless.
eSATA - This is the same as SATA just for external devices using SATA technology.
The first thing I look for in a mainboard is the brand name. My first choice is Asus. The new Gigabyte boards are good as well, they have come along way in the last year or so.
I always go with a board that has gigabit lan, has raid support built in, PCI express for my video card, and on board sound. It should also have the ability to change clock speeds in the bios. This option is not just for overclocking, some memory and components require different voltages and special settings, this way you know it is supported by the board you choose.
How much you spend on the board is up to you, if you need a general guide line so you stay in your budget, I typically try to shoot for about 40% of my budget for the CPU and the motherboard.
Make sure the CPU you are picking is supported. If you go to the manufacturers website, there will be a link that will tell you what processors are supported by the board you are interested in. Before you buy, read the reviews, more information on that can be found on the How To Build A Computer page.