A 29er wheelset refers to two 29 inch wheels as opposed to the industry standard 26 inch wheels. Specialty frames have to be used to accommodate the wheels and they are not for everyone. They typically work better for larger riders although there is a strong following of riders of many sizes.
A 29er wheelset gives the bike a higher ride height and the wheels are able to roll over larger objects and obstacles easier than with a 26 inch wheel. This is known as the angle of attack and can make riding easier and harder depending on the situation.
A 29er wheelset can achieve higher speeds and hold that speed easier but they are harder to get up to speed and harder to slow down. They are popular on cyclocross bikes, large riders as well as single speed bicycles.