These are not quite as important, but may still have a major effect on your motherboard decision.
Maximum Memory Supported: You want to make sure your motherboard supports at least as much RAM as you are planning to buy. As of early 2009, make sure it supports at least 4-8gb, but 16 gb is better.
Onboard Video: If you do not want to buy a video card, check for onboard video. If you plan to use the PC for gaming or video/photo editing, you probably want NO onboard video. You will buy your own graphics card, and it is better to not even have to bother with disabling the onboard. Onboard video is generally very poor and completely unsuited to gaming.
Onboard LAN: It is convenient that most motherboards have onboard LAN now (usually 10/100/1000Mbps). If you do not have this, you will need to buy an ethernet card if you plan to use this computer on the internet (if you are reading this, I imagine you will want that).
Onboard Sound: Onboard sound is becoming more common now that many games, applications, and operating systems have good sound support. The need for a hardware sound card is certainly diminishing. For gaming, a sound card is still recommended, however, as some games have conflicts and other problems with onboard sound. If you are not a heavy gamer, onboard sound is fine.
Ports: Simply check to make sure it has enough USB, PS/2, or other ports you want for external peripherals.
This changes often, so instead of making a specific recommendation I am going to point you to place you can go for this information.
PC Gamer has a section in every edition of their magazine called "HARD STUFF." This is their hardware section. In that section there is usually an article called "HARD STUFF TRINITY." This is basically a list of specific hardware suggestions for DREAM, MID-RANGE, and ENTRY LEVEL gaming PCs. Their suggestions are often very good.
The Guru of 3D is an excellent web site with an enormous amount of information about computer hardware. As the title implies, it is biased towards gaming or people who do anything graphics heavy. Every few months the author updates his buyers guides, and I have found them to be very useful. His December 2008 buyer's guide begins here.
There are a number of online retailers that have an excellent selection of motherboards. As with any online shopping, pay close attention to return policies, warranties, and any guarantees.
Pricewatch is a good general site for doing price comparisons. Pricewatch is a meta-site that grabs price information from many online retailers. You cannot actually buy anything from Pricewatch.
Newegg is an online computer/electronics store that generally has excellent prices and a good reputation. I have shopped there many times and have had good experiences. Each product entry at Newegg has very detailed hardware specifications (click the SPECIFICATIONS tab for the info) as well as tons of customer reviews. The customer reviews also sometimes include tips about a specific product that may help you make a decision.
I believe that covers everything. Once you get your motherboard, remember that installing the CPU is one of the most delicate parts of assembling your PC. Read the instructions carefully before you do the CPU install and then work with caution.
An excellent step by step guide (with pictures) on how to actually build a PC can be found here.
Good luck and enjoy your new motherboard!