What is the difference between motherboards?

More features(more then one video card slot, more usb3, ect) and most times a better power deliver(more phases with better control) and cooling(vrm heatsinks) system for that power delivery system(more extreme overclocking room).

Warranty may also be longer in some cases.

If you do not NEED these features, you will be fine with a cheaper board in many cases. My basic(h55n usb3) gigabyte board has been holding up just fine.

Basic no fancy cooling, but works
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More fancy. built in wireless and vrm cooling. May have come with X-fi MB audio software as well
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In theory, higher quality parts (capacitors, power delivery, etc). In reality, not much in terms of performance for the average user. You can see a wide range of boards compared at the link below. Basically, for general purpose computing and gaming (unless you need to run 3 or 4 high end GPUs) a $400 board doesn't get you anything over a ~150 (maybe less) board. Mine was $90 in a combo deal at Microcenter and it does everything I need it to do.

Just make sure you get one with the right connectors for you (e.g. some folks needs FireWire).

http://www.anandtech.com/show/6697/asrock-fatal1ty-x79-champion-and-x79-professional-review-from-a-gamer-to-gamers/11

Edit: I've never paid for a high end board over the past 17 years and have never had one fail (ASRock, ASUS, MSI, and Gigabyte).