[Pilot_51]

Motherboards aren't the expensive part, but they aren't much cheaper than anything else if you're going for budgeted performance. The mobo is also a very important part for compatibility and staying up to date, because they include lots of different standards and if a new one comes out (USB2, PCI-E, and SATA are good examples) the board becomes outdated, other hardware usually only gets outdated in one or two aspects and they last about as long as mobo's before getting really outdated.
I suggest always staying away from pre-built systems and learn to build them yourself if you want to save money, not only will it get rid of all the extra junk software, but you'll have 100% choice on what hardware and where you buy from, so you could choose increased or decreased performance for different parts as your budget and needs require, likely saving a couple thousand bucks on a high-end system. If you don't have money to throw away and aren't totally disparate for the latest and greatest, pick hardware somewhere between 6-18 months old, because the prices would've seriously dropped to make room for the latest hardware and you'll still have decent performance for the latest games.