Your question's a bit wide open and undefined. You need to answer a couple of questions for yourself, first. The most important ones are whether you want go with an AMD or Intel CPU, and which model. Everything else follows from that.
You have to decide between 32 adn 64 bit processors and higher performance (Athlon/Pentium) or lower cost (Duron/Celeron) chips. Base your decision on what you intend to be doing with your system. A system that would be overkill for general office work may not be good enough for graphic design, audio-video production or high level gaming. If you intend to use this system as part of what you do for your income, spending too little on an inadequate machine can be as costly as spending too much.
Once you determine the basics, check reviews of the latest boards for performance, features and support for the peripherals you intend to use. For example, most new boards come with onboard LAN, but some support Gigabit LAN, while most only support T10/100. Most new boards support USB2, but some have more ports than others. Most new motherboards support AGP 8, but some only support AGP 4. Most boards have onboard sound, but some are only support minimum AC97, and some have built in high end sound processors, and of those, some have known problems.
Also, if you need a high end graphic card, know which video cards support your intended applications and whether there are any known compatibility issues between the vid card you want to use and any motherboard you are considering.
It will be easier to give you meaningful feedback once you've defined your needs and started with a list of components you think might meet them.
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