Some motherboard basics:
There are two ways to select a motherboard. Either you start with it, or you're matching it to components you already have or know you want to get. Whichever path you take, here is some basic information to help you.
You start out at a fork in the road. Intel or AMD? From there you determine the socket type. Right now, AMD's Sockets 939 and AM2 are very popular, as is Intel's LGA775. If you're fairly fresh to the guts of a computer, you'll probably be swimming in a big puddle of socket goo. Don't worry. The most important thing at this point is to make sure the motherboard supports the CPU, or vice versa. If you're browsing online retailers, the socket type should be easy to identify on both components.
The next step revolve around the size of the motherboard:
Common Motherboard Form Factors
For more information, check out motherboard form factors
At this point, you want to make sure your motherboard is supported by the case you want or will use. Most ATX cases will also have screw mounts for mATX boards. Some will just be riddled with screw mounts to support more than the ATX form factor.
If you don't know much about motherboards, browse the many boards on sites such as Newegg
and look at the pictures. Most have labels for the different parts commonly found on motherboards. These include RAM slots (DIMMs), SATA and IDE ports, AGP and PCI/PCI-E slots, etc. You could also factor in RAID support.
Depending on your budget and/or needs, a video card may be desired. If you plan to buy one, you'll save time by looking only at motherboards without
onboard/integrated video. If your budget's tight, and your gaming is non-existent or as extensive as Solitaire and maybe a fancy screensaver, onboard video is perfect for you.
Aside from a good power supply, the (aptly named) motherboard is the center and easily the most important component in a system. This is so because it facilitates everything connected to it.
Regarding overclocking, if you plan to OC, you'll want to make sure the board you have your eye(s) on is good for it. Some boards flat-out suck. Some boards are okay, but probably won't push your CPU/RAM very much before becoming unstable. Some boards are rock-solid for overclocking. The best way to determine is to Google the board and/or hop onto a good forum and ask around. You'll want more than just the reviews on retailer sites.
Overclocking (OCing) can apply to your CPU, RAM, and graphics port(s). This basically means changing the voltage the motherboard applies to these components. People most commonly overclock their CPU. Many also overclock their RAM to achieve better timings. I do not recommend overclocking graphics ports. Doing so carries the most risk. Do so only if you're an expert, filthy rich, a computer/electric/mechanical engineering student, or it's on old, cheap components.
Overclocking doesn't appeal to everyone. Don't brush off a motherboard because it has bad reviews. Sometimes the bad reviews are regarding its ability to overclock. If you don't plan to OC, chances are it's still a good board to run your components at stock speeds.
The following list is in no particular order, and all brands are going to have sub par and great boards. Don't blindly buy a motherboard. Definitely do your research (like you should for everything).
Go-to Motherboard Brands
Usually you also can expect good things from Gigabyte and Foxconn, and maybe Biostar. There's also Elitegroup, but I don't know much about them.
I know I'm leaving out a bunch of stuff. I'm at work, and now I gotta do some work. Should give you a good start though.