GETTING STARTED
The Motherboard is the most important component in your computer system. It is the backbone that supports all the other computer components. Choosing the right motherboard will be the difference between allowing your components to work at their maximum capacity or significantly slowing them down.
As far as Motherboards go you're getting off easy. The trend towards further integration is continuing, this means more and more components are now bundled into the motherboard. Right now a consumer can get a decent Motherboard that integrates all video, sound ,and modem, functions. This makes for a cheaper and more efficient system. The tradeoff however is that most integrated components are only meant for basic use and are not as powerful as some of the stand alone versions. If you are a serious graphics or audio user, (I.E. Gamer, Musician, Video Editor ETC...) steer clear of the integrated components and get the Graphics and Sound Card that will suit your purpose.
WHAT TO LOOK FOR ATX
Just about all Motherboards today are of the ATX variety. Make sure yours is.
PROCESSOR
Make sure you get the right Motherboard for the processor you are going to install onto it. There are four classes of processor in use today,Socket 370, Slot 1, Slot A and Socket A. There are other older formats that are in use today but we are discussing current components and what is currently being Manufactured and Marketed today. In these Sockets you'll place either an AMD or INTEL Processor. More about that in the CPU section.
MOTHERBOARD SPEED
Motherboards can currently run at speeds of 100MHz with newer boards running at higher speeds. Get the fastest one you can afford, as everything on the Motherboard can only operate as fast as the Motherboard itself.
MEMORY Motherboards today use Memory modules called DIMMS. DIMMS are normally PC100 (That means they run at 100MHz), but PC133's (That logically means that they run at 133MHz)are becoming more and more prevalent , but are a bit more expensive. Make sure when you buy a PC133 DIMMS your Motherboard can accommodate it, otherwise it will only run at the lowest speed it is capable of running. (Probably 100MHz). Newer AMD systems run on a faster and more expensive version of memory known as DDR SDRAM Newer Intel systems have what is known as RDRAM. These guys are FAST! but (and here's the rub) EXPENSIVE!, if your daddy's rich and your ma is good looking I say go for it. The rest of us poor schmucks will just have to mosey along.
BUS TYPE A Bus on a computer is sort of a pipeline your Motherboard uses to transfer information between the processor and the computers other components as quickly as it can. This being said, Not all Busses were created equal. (If you want to get racy you can say that they have different "Bus" sizes)
The ISA Bus
The ISA Bus is the Granddaddy of Busses and was Introduced by IBM in the mid-eighties. Back then it was considered cutting edge (1984 was about a thousand years ago in computer years however). Today it is considered a teeter-tottering relic that just likes to get in the way of everything. You can recognize the ISA slots because they are the longest slots on your Motherboard. It will probably be on your Motherboard and you probably WILL have to wrangle with it some down the road as it tries to hog your system resources. There will probably be two ISA slots on your Motherboard, try to give them as much respect as possible and stay away from them.
The PCI Bus
The PCI bus is today's standard, and for good reason. Cards that are used in them are smaller, faster, less resource hungry and (gasp!) cheaper than those meant for ISA slots. They are situated next to the ISA slots on the Motherboard. Almost all computer cards (excepting Graphics cards which use an AGP slot) manufactured today are of the PCI variety. If you have an old ISA sound or modem card lying around and you want to save a buck or two then by all means use it, just be prepared to do some IRQjuggling.
The AGP Bus
AGP is a bus that was manufactured strictly for High-Speed Graphics. The AGP slot is even smaller than the PCI slot and usually sits by itself next to the PCI slots. Motherboards today include an AGP slot.High end users want to make sure that their motherboard can accomodate 2x and 4x AGP cards. (2x and 4x are EVEN FASTER forms of AGP allowing for much much higher splatter rates in shoot em up games.)
PLUG AND PLAY Your Motherboard has it. All Motherboards with PCI slots have to be Plug and Play compatible (PNP). Plug and Play is a format that allows a peripheral to be automatically detected by the system which then installs the necessary drivers.
CHIPSET Use a High quality Chipset, From a reputable manufacturer. Let me take this opportunity to further stress; your computer will only be as fast as your Motherboard will let it be. If you have to splurge on one thing, make it the Motherboard. Also, make sure that if Technical support is needed you are able to obtain it.