When bilding a custom computer the CPU and motherboard are the two most important components. The main focus in deciding what type of motherboard is narrowing down which specific processor that will be installed. The faster the CPU then the more options become available, thus most manufacturers will supply appropriate options. At NTCPU we go into this in depth in our eBook about building CUSTOM CPU's. A recommende brand is ASUS due to their constant efforts to be a leader and also ading newer technologies as standards at affordable prices.
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The argument is everlasting about what would be considered best for gaming, but I will attempt to give you tactical information. The Intel based setup has the better stepping technology in terms of calculations per second, but it was mainly designed to multitask and run operating system data across networks. Since Intel is better suited to NVidia graphics systems, the partnership can prove to be quite vigorous for hardcore gamers.
Although, AMD and ATI have worked hand in hand for quite a number of years and they have the better partnership, therefore as a gaming system, it would be quite formidable against even a top spec Intel based setup. My personal choice is the latter, as I only run a small home network of 4 computers and my personal graphic and audio demands are quite high. If they were higher for faster file processing and better data management than gaming, multimedia and graphics, then I would lean more towards Intel and NVidia.